Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 116 of 143
Found at i:35352140 original size:76 final size:76
Alignment explanation
Indices: 35352010--35352620 Score: 906
Period size: 76 Copynumber: 8.0 Consensus size: 76
35352000 TCAACCGCAC
* *
35352010 CAAGATCATTTCCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAATGAA-TCTTTATCTCTGAA
1 CAAGATCATTT-CCTATCCTCTTGAAATTGAAGTAAAGTTGGATAA-CAAGTCTTTATCTCTGAA
35352074 ATTGAAGTAAGAG
64 ATTGAAGTAAGAG
* * * *
35352087 CAAGATCTTTTCCTGTCCGT-TTGAAATTGAAGTAGAGTTGGACAACAAGTCTTTATCTCTGAAA
1 CAAGATCATTTCCTATCC-TCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAA
35352151 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* *
35352163 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
35352227 TGAAGTAAGAG
66 TGAAGTAAGAG
* * * *
35352238 CAAGATCATTCCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACGAGTCGTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
35352303 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
35352314 CAACATCATTCCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
35352379 TGAAGTAAGAG
66 TGAAGTAAGAG
* ** * * *
35352390 CAAGATCA-TGCCATATCCTCTTGAAATTGAAGTAAAGTTGGATATTAAGTATCTATCTCTAAAA
1 CAAGATCATTTCC-TATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAA
35352454 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* ** *
35352466 CAAGATCATTTCATATCCTCTTGAAATTGAAGTAAAGTTGGATAATGAGTCTTTATCTCTGAAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
35352531 TGAAGTAAGAG
66 TGAAGTAAGAG
* * * *
35352542 CAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
35352607 TGAAGTAAGAG
66 TGAAGTAAGAG
35352618 CAA
1 CAA
35352621 AATGAAGCCT
Statistics
Matches: 489, Mismatches: 39, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
75 78 0.16
76 398 0.81
77 13 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (76 bp):
CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:35352150 original size:38 final size:36
Alignment explanation
Indices: 35352108--35352615 Score: 171
Period size: 38 Copynumber: 13.4 Consensus size: 36
35352098 CCTGTCCGTT
35352108 TGAAATTGAAGTAGAGTTGGACAACAAGTCTTTATCTC
1 TGAAATTGAAGTA-AG-TGGACAACAAGTCTTTATCTC
* * ** *
35352146 TGAAATTGAAGTAAGAGCA-AGATCATTTC-CTATCCTC
1 TGAAATTGAAGTAAGTGGACA-A-CAAGTCTTTAT-CTC
* *
35352183 TTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 -TGAAATTGAAGTA-AGTGGACAACAAGTCTTTATCTC
* * * **
35352221 TGAAATTGAAGTAAG-AG-CAAGATCATTCCCTATCCTC
1 TGAAATTGAAGTAAGTGGACAACA--AGTCTTTAT-CTC
* * *
35352258 TTGAAATTGAAGTAGAGTTGGATAACGAGTCGTTATCTC
1 -TGAAATTGAAGTA-AG-TGGACAACAAGTCTTTATCTC
* * **
35352297 TGAAATTGAAGTAAG-AG-CAACATCATTCCCTATCCTC
1 TGAAATTGAAGTAAGTGGACAACA--AGTCTTTAT-CTC
*
35352334 TTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGT-AAG-TGGACAACAAGTCTTTATCTC
* * * **
35352373 TGAAATTGAAGTAAGAGCA-AGATCATG-CCATATCCTC
1 TGAAATTGAAGTAAGTGGACA-A-CAAGTCTTTAT-CTC
* ** * *
35352410 TTGAAATTGAAGTAAAGTTGGATATTAAGTATCTATCTC
1 -TGAAATTGAAGT-AAG-TGGACAACAAGTCTTTATCTC
* * * ** *
35352449 TAAAATTGAAGTAAGAGCA-AGATCATTTC-ATATCCTC
1 TGAAATTGAAGTAAGTGGACA-A-CAAGTCTTTAT-CTC
* **
35352486 TTGAAATTGAAGTAAAGTTGGATAATGAGTCTTTATCTC
1 -TGAAATTGAAGT-AAG-TGGACAACAAGTCTTTATCTC
* * *
35352525 TGAAAATGAAGTAAG-AG-CAA-GA-TCGTTTCCCATCCTC
1 TGAAATTGAAGTAAGTGGACAACAAGTC-TTT---AT-CTC
* *
35352562 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGT-AAG-TGGACAACAAGTCTTTATCTC
35352601 TGAAATTGAAGTAAG
1 TGAAATTGAAGTAAG
35352616 AGCAAAATGA
Statistics
Matches: 346, Mismatches: 73, Indels: 103
0.66 0.14 0.20
Matches are distributed among these distances:
32 2 0.01
33 5 0.01
34 8 0.02
35 6 0.02
36 33 0.10
37 56 0.16
38 151 0.44
39 41 0.12
40 26 0.08
41 5 0.01
42 7 0.02
43 4 0.01
44 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (36 bp):
TGAAATTGAAGTAAGTGGACAACAAGTCTTTATCTC
Found at i:35353761 original size:16 final size:16
Alignment explanation
Indices: 35353740--35353777 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35353730 TTAACAATAA
*
35353740 TAATAATA-TTTTTAAT
1 TAATAATAGTATTT-AT
35353756 TAATAATAGTATTTAT
1 TAATAATAGTATTTAT
35353772 TAATAA
1 TAATAA
35353778 CATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TAATAATAGTATTTAT
Found at i:35353761 original size:19 final size:20
Alignment explanation
Indices: 35353737--35353775 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
35353727 ATATTAACAA
35353737 TAATAATAATATTT-TTAAT
1 TAATAATAATATTTATTAAT
*
35353756 TAATAATAGTATTTATTAAT
1 TAATAATAATATTTATTAAT
35353776 AACATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TAATAATAATATTTATTAAT
Found at i:35354791 original size:59 final size:58
Alignment explanation
Indices: 35354726--35355568 Score: 966
Period size: 59 Copynumber: 14.4 Consensus size: 58
35354716 CCTGGACTAT
*
35354726 CCAAAAATTACCATTTTAGCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
35354785 CTAAAAATTACCATTTTAGCTCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
35354844 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTT-A
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * ** * *
35354902 TCAAAAATTATCGTTTTACCCCCAAACTTTTTAAAATCCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * * * ** *
35354961 CCCAAAATAACCATTTTATCCACGAACTTTTCAAAATTTCATTTTTAACCCTAATTTTA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
35355020 CCAAAAATTACTATTTTACCCCCGAACTTTCCAAAA-TCCTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCA
* *
35355079 CCAAAAATTACCAGTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
35355137 TCAAAAATTACCATTTTACCCCTAAACTTTTCAAAATCCCATTTTTAACCCCCATTTCA
1 CCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
35355196 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCTAATTTTAACCTCGACTTCA
1 CCAAAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
35355255 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATCCCATTTTTAACCCCGA-TTCA
1 CCAAAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
35355313 CCAAAAATTACCGTTTTATCCCAGAACTTTCCAAAATTCCCTTTTTAA-CCCGATTTCA
1 CCAAAAATTACCATTTTACCCCA-AACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * * *
35355371 CCGAAAATTACCATTTTAGCCTCGAACTTTCCAAAATTTCATTTTTAATCCTGATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
35355430 CC-AAAATTACCATTTTACCCCTGAACTTTCCAAAATTTCATTTTAAACCTCGATTCCA
1 CCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
35355488 CCAAAAATTACCGTTTTATCCTCAAACTTTCCAAAATTCCCTTTTTAACCTCGAATTTTC-
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCCG-A-TTTCA
35355548 CC-AAAATTA-CATTTATACCCC
1 CCAAAAATTACCATTT-TACCCC
35355569 TCGAGAGTCA
Statistics
Matches: 675, Mismatches: 93, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
57 9 0.01
58 250 0.37
59 404 0.60
60 9 0.01
61 3 0.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:35354974 original size:117 final size:116
Alignment explanation
Indices: 35354726--35355568 Score: 955
Period size: 117 Copynumber: 7.2 Consensus size: 116
35354716 CCTGGACTAT
* * *
35354726 CCAAAAATTACCATTTTAGCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACTAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCCGATTT-ACCAAAA
* * * *
35354791 ATTACCATTTTAGCTCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
64 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
*
35354844 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTATCAAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC-CGATTTACCAAAAA
* * ** *
35354909 TTATCGTTTTACCCCCAAACTTTTTAAAATCCCATTTTTAACCCCAATTTCA
65 TTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * * * * * * *
35354961 CCCAAAATAACCATTTTATCCACGAACTTTTCAAAATTTCATTTTTAACCCTAATTTTACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCC-GA-TTTACCAAAA
* * * *
35355026 ATTACTATTTTACCCCCGAACTTTCCAAAATCCTATTTTTAACCTCGATTTCA
64 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * *
35355079 CCAAAAATTACCAGTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCTGATTTCATCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCC-GATTT-ACCAAAA
* * *
35355143 ATTACCATTTTACCCCTAAACTTTTCAAAATCCCATTTTTAACCCCCATTTCA
64 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
** * * *
35355196 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCTAATTTTAACCTCGACTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC-CGA-TTTACCAAAA
**
35355261 ATTACCATTTTACCCTTAAACTTTCCAAAATCCCATTTTTAACCCCGA-TTCA
64 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * * *
35355313 CCAAAAATTACCGTTTTA-TCCCAGAACTTTCCAAAATTCCCTTTTTAACCCGATTTCACCGAAA
1 CCAAAAATTACCATTTTACCCCCA-AACTTTCCAAAATTCCATTTTTAACCCGATTT-ACCAAAA
* * * ** * *
35355377 ATTACCATTTTAGCCTCGAACTTTCCAAAATTTCATTTTTAATCCTGATTTCA
64 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
** * * *
35355430 CC-AAAATTACCATTTTACCCCTGAACTTTCCAAAATTTCATTTTAAACCTCGATTCCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC-CGATT-TACCAAAA
* * * *
35355494 ATTACCGTTTTATCCTCAAACTTTCCAAAATTCCC-TTTTTAACCTCGAATTTTC-
64 ATTACCATTTTACCCCCAAACTTTCCAAAA-TCCCATTTTTAACCCCG-A-TTTCA
35355548 CC-AAAATTA-CATTTATACCCC
1 CCAAAAATTACCATTT-TACCCC
35355569 TCGAGAGTCA
Statistics
Matches: 618, Mismatches: 90, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
115 2 0.00
116 93 0.15
117 300 0.49
118 216 0.35
119 7 0.01
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (116 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCGATTTACCAAAAAT
TACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:35355025 original size:176 final size:177
Alignment explanation
Indices: 35354726--35355568 Score: 1030
Period size: 176 Copynumber: 4.8 Consensus size: 177
35354716 CCTGGACTAT
* *
35354726 CCAAAAATTACCATTTTAGCCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACTAAA
1 CCAAAAATTACCATTTTA-CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAA
* * *
35354790 AATTACCATTTTAGCTC-CAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAAATTA
65 AATTACCATTTTATC-CACAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTA
35354854 CCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTT-A
129 CCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * * * ** * * *
35354902 TCAAAAATTATCGTTTTACCCCCAAACTTTTTAAAATCCCATTTTTAACCCCAATTTCACCCAAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * * * * *
35354967 ATAACCATTTTATCCACGAACTTTTCAAAATTTCATTTTTAACCCTAATTTTACCAAAAATTACT
66 ATTACCATTTTATCCACAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACC
*
35355032 ATTTTACCCCCGAACTTTCCAAAA-TCCTATTTTTAACCTCGATTTCA
131 ATTTTACCCCCAAACTTTCCAAAATTCC-ATTTTTAACCTCGATTTCA
* * *
35355079 CCAAAAATTACCAGTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCTGATTTCATCAAAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * *
35355143 ATTACCATTTTA-CCCCTAAACTTTTCAAAATCCCATTTTTAACCCCCATTTCACCAAAAATTAC
66 ATTACCATTTTATCCAC-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTAC
** * * *
35355207 CATTTTACCCTTAAACTTTCCAAAATTCTAATTTTAACCTCGACTTCA
130 CATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
35355255 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATCCCATTTTTAACCCCGA-TTCACCAAAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * *
35355319 ATTACCGTTTTATCC-CAGAACTTTCCAAAATTCCCTTTTTAA-CCCGATTTCACCGAAAATTAC
66 ATTACCATTTTATCCACA-AACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTAC
* * * *
35355382 CATTTTAGCCTCGAACTTTCCAAAATTTCATTTTTAATCCT-GATTTCA
130 CATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAA-CCTCGATTTCA
* * * * *
35355430 CC-AAAATTACCATTTTACCCCTGAACTTTCCAAAATTTCATTTTAAACCTCGATTCCACCAAAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * *
35355494 ATTACCGTTTTATCCTCAAACTTTCCAAAATTCCCTTTTTAACCTCGAATTTTC-CC-AAAATTA
66 ATTACCATTTTATCCACAAACTTTCCAAAATTCCATTTTTAACC-CCAA-TTTCACCAAAAATTA
35355557 -CATTTATACCCC
129 CCATTT-TACCCC
35355569 TCGAGAGTCA
Statistics
Matches: 574, Mismatches: 77, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
174 45 0.08
175 123 0.21
176 349 0.61
177 53 0.09
178 4 0.01
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (177 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
ATTACCATTTTATCCACAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACC
ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:35355533 original size:29 final size:30
Alignment explanation
Indices: 35355199--35355557 Score: 91
Period size: 29 Copynumber: 12.3 Consensus size: 30
35355189 CATTTCACCA
* * *
35355199 AAAATTACCATTTTACCCTTAAACTTT-CC
1 AAAATTACCGTTTTAACCTCAAACTTTCCC
** *
35355228 AAAATT-CTAATTTTAACCTC-GAC-TTCACC
1 AAAATTAC-CGTTTTAACCTCAAACTTTC-CC
* * *
35355257 AAAAATTACCATTTTACCCTTAAACTTT-CC
1 -AAAATTACCGTTTTAACCTCAAACTTTCCC
* * **
35355287 AAAA-TCCCATTTTTAACC-CCGA--TTCACC
1 AAAATTACC-GTTTTAACCTCAAACTTTC-CC
*
35355315 AAAAATTACCGTTTTATCC-CAGAACTTT-CC
1 -AAAATTACCGTTTTAACCTCA-AACTTTCCC
* * *
35355345 AAAATTCCCTTTTTAACC-C-GA-TTTCACC
1 AAAATTACCGTTTTAACCTCAAACTTTC-CC
* * *
35355373 GAAAATTACCATTTTAGCCTCGAACTTT-CC
1 -AAAATTACCGTTTTAACCTCAAACTTTCCC
* ** *
35355403 AAAATTTCATTTTTAATCCT--GA-TTTCACC
1 AAAATTACCGTTTTAA-CCTCAAACTTTC-CC
* * *
35355432 AAAATTACCATTTT-ACCCCTGAACTTT-CC
1 AAAATTACCGTTTTAACCTC-AAACTTTCCC
* * * *
35355461 AAAATT-TCATTTTAAACCTC-GA-TTCCACC
1 AAAATTACCGTTTT-AACCTCAAACTTTC-CC
*
35355490 AAAAATTACCGTTTTATCCTCAAACTTT-CC
1 -AAAATTACCGTTTTAACCTCAAACTTTCCC
* * * *
35355520 AAAATTCCCTTTTTAACCTCGAATTTTCCC
1 AAAATTACCGTTTTAACCTCAAACTTTCCC
35355550 AAAATTAC
1 AAAATTAC
35355558 ATTTATACCC
Statistics
Matches: 241, Mismatches: 52, Indels: 73
0.66 0.14 0.20
Matches are distributed among these distances:
26 5 0.02
27 10 0.04
28 20 0.08
29 128 0.53
30 56 0.23
31 13 0.05
32 9 0.04
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACCGTTTTAACCTCAAACTTTCCC
Found at i:35355608 original size:28 final size:29
Alignment explanation
Indices: 35355548--35355609 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
35355538 TCGAATTTTC
*
35355548 CCAAAATTACATTTATACCCCTCGAGAGT
1 CCAAAATTACATTTATACCCCTCGAGAAT
35355577 -CAAAATTACCATTT-TACCCC-C-AGATAT
1 CCAAAATTA-CATTTATACCCCTCGAGA-AT
35355604 CCAAAA
1 CCAAAA
35355610 GTCTCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 3 0.10
27 2 0.07
28 19 0.66
29 5 0.17
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.26
Consensus pattern (29 bp):
CCAAAATTACATTTATACCCCTCGAGAAT
Found at i:35358570 original size:2 final size:2
Alignment explanation
Indices: 35358563--35358599 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
35358553 TCTTCCCTTT
*
35358563 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35358600 TAAGAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35359474 original size:26 final size:26
Alignment explanation
Indices: 35359416--35359474 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
35359406 GGATTTGATG
* *
35359416 ATGTGGGACGTGATGACGTGGCAGCTG
1 ATGT-GGACGTGATGACATGGCAGCTA
* * *
35359443 ACGTGGACGTGCTGACATGGTAGCTA
1 ATGTGGACGTGATGACATGGCAGCTA
35359469 ATGTGG
1 ATGTGG
35359475 CGGCTTAGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.24
Consensus pattern (26 bp):
ATGTGGACGTGATGACATGGCAGCTA
Found at i:35359599 original size:6 final size:6
Alignment explanation
Indices: 35359588--35359622 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
35359578 CAATTAAACT
*
35359588 TTTAAA TTTAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35359623 CTCCAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:35359618 original size:11 final size:12
Alignment explanation
Indices: 35359590--35359622 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
35359580 ATTAAACTTT
*
35359590 TAAATTTAAATT
1 TAAATTTAAATA
35359602 TAAATTTAAA-A
1 TAAATTTAAATA
35359613 TAAATTTAAA
1 TAAATTTAAA
35359623 CTCCAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:35359618 original size:17 final size:17
Alignment explanation
Indices: 35359596--35359681 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
35359586 CTTTTAAATT
35359596 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* **
35359613 TAAATTTAAACTCCAAA
1 TAAATTTAAATTTAAAA
** *
35359630 TAAGCTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
35359647 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
*
35359664 TGAA-TTAAGATTTAAAA
1 TAAATTTAA-ATTTAAAA
35359681 T
1 T
35359682 CTAAAGTTTT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
16 4 0.08
17 49 0.92
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:35360335 original size:78 final size:77
Alignment explanation
Indices: 35360247--35360406 Score: 180
Period size: 78 Copynumber: 2.1 Consensus size: 77
35360237 ATCACTTCAA
* * * ** *
35360247 ATGATGATCTGCCTCAAGCTTGA-GGTAAGAGA-CTGAATGGTTGCAATCTGCCTTAGGCTCGGG
1 ATGATGATCTGCC-CAAGCTTCAGGGTAAAAGATC-AAATGACTGCAATCTGCC-CAGGCTCGGG
*
35360310 GTAAGAGATTTGCTG
63 GTAAGAGATTGGCTG
* * *
35360325 ATGATGATCTGCCCCAGGTTCAGGGTAAAAGATCAAATGACTGCAATTTGCCCAGGCTCGGGGTA
1 ATGATGATCTGCCCAAGCTTCAGGGTAAAAGATCAAATGACTGCAATCTGCCCAGGCTCGGGGTA
*
35360390 AGAGATTGGTTG
66 AGAGATTGGCTG
35360402 ATGAT
1 ATGAT
35360407 TTAACTTCAC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
77 33 0.48
78 35 0.51
79 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (77 bp):
ATGATGATCTGCCCAAGCTTCAGGGTAAAAGATCAAATGACTGCAATCTGCCCAGGCTCGGGGTA
AGAGATTGGCTG
Found at i:35360689 original size:92 final size:92
Alignment explanation
Indices: 35360479--35360834 Score: 626
Period size: 92 Copynumber: 3.9 Consensus size: 92
35360469 CTAATTTCGT
* * * *
35360479 TGCATCTTCAAGAAGATAGGATTTGATG-TTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAG
1 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
* *
35360543 AGATAAAG-TTTACTATCCAACTTTAC
66 AGATAAAGACTTGCTATCCAACTTTAC
35360569 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
1 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
35360634 AGATAAAGACTTGCTATCCAACTTTAC
66 AGATAAAGACTTGCTATCCAACTTTAC
35360661 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
1 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
35360726 AGATAAAGACTTGCTATCCAACTTTAC
66 AGATAAAGACTTGCTATCCAACTTTAC
* *
35360753 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTATTATAACTTCAGAG
1 TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
35360818 AGATAAAGACTTGCTAT
66 AGATAAAGACTTGCTAT
35360835 TGTTTTTTAT
Statistics
Matches: 256, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
90 25 0.10
91 43 0.17
92 188 0.73
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (92 bp):
TGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCAGAG
AGATAAAGACTTGCTATCCAACTTTAC
Found at i:35361067 original size:50 final size:49
Alignment explanation
Indices: 35360954--35361299 Score: 381
Period size: 50 Copynumber: 7.0 Consensus size: 49
35360944 CCTTCAAATC
* * * * *
35360954 TTCGTGGTACTGGATCCGCCGTCGCGGCTTAGATATTTCCCTTCATGTC
1 TTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
* * * * *
35361003 TTCGCGGTATTGGATTCGCCGTTGTGGTTTTAGATCTTTCCCGTCGTGTT
1 TTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCGTCGTGTT
* * * * *
35361053 TTCGTGGTACTGGATCTGCCGTTGCGGCTTAGATATTT-CCTTGGTGTC
1 TTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
* * * * *
35361101 TTCGTGGTACTGGATCCGCCGTCGTGGCTTAGATATTTCCC-TTGTGTC
1 TTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
* * *
35361149 TTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCCTGTCGTGTT
1 TTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCGTCGTGTT
* ** *
35361199 TTTGTGGTACTGGATCCGTTGTTGCGGCCTTAGATCTTTACCGTCGTGTT
1 TTCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCCGTCGTGTT
* *
35361249 TTCGTGGTACTGGATCCACCGTTGCGGCTTTAGATCTTTCCCGTTGTGTT
1 TTCGTGGTACTGGATCCGCCGTTGCGGC-TTAGATCTTTCCCGTCGTGTT
35361299 T
1 T
35361300 CATGGTGTTG
Statistics
Matches: 246, Mismatches: 46, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
48 71 0.29
49 46 0.19
50 129 0.52
ACGTcount: A:0.10, C:0.23, G:0.27, T:0.40
Consensus pattern (49 bp):
TTCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
Found at i:35366821 original size:147 final size:146
Alignment explanation
Indices: 35366571--35366845 Score: 392
Period size: 147 Copynumber: 1.9 Consensus size: 146
35366561 CTTGGATACC
** * * *
35366571 CGAGGACAAAATGGTAATTTTGGACTCTCGGGAGAAAAATGATAATTTTGGAAAAATTTAGGGTT
1 CGAGGACAAAATGGTAATTTTAAACTCTCGAGAGAAAAATGATAATTTGGGAAAAATTTAGAGTT
* * * *
35366636 AAAAAATGATATTTTAGACACTTAAGGGTAAAATGGTAA-TTTTAAAAAGAATCAGGATCAAAAC
66 AAAAAATGACATTTTAAACACTTAAGGGTAAAACGGTAATTTTTAAAAA-AATCAAGATCAAAAC
35366700 GAGACTTTTTAGATGTT
130 GAGACTTTTTAGATGTT
* *
35366717 CGAGGGCAAAATGGTAATTTTAAACTTTCGAGAGGAAAAATGATAATTTCGGGAAAAATTTAGAG
1 CGAGGACAAAATGGTAATTTTAAACTCTCGAGA-GAAAAATGATAATTT-GGGAAAAATTTAGAG
* *
35366782 TT-AAAAATGACATTTTAAACACTTGAGGGTAAAACGGTAATTTTTAGAAAAATCAAGATCAAAA
64 TTAAAAAATGACATTTTAAACACTTAAGGGTAAAACGGTAATTTTTAAAAAAATCAAGATCAAAA
35366846 ATGAGATTTT
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
146 28 0.25
147 62 0.55
148 23 0.20
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (146 bp):
CGAGGACAAAATGGTAATTTTAAACTCTCGAGAGAAAAATGATAATTTGGGAAAAATTTAGAGTT
AAAAAATGACATTTTAAACACTTAAGGGTAAAACGGTAATTTTTAAAAAAATCAAGATCAAAACG
AGACTTTTTAGATGTT
Found at i:35366875 original size:147 final size:146
Alignment explanation
Indices: 35366571--35366884 Score: 391
Period size: 147 Copynumber: 2.1 Consensus size: 146
35366561 CTTGGATACC
* ** * * *
35366571 CGAGGACAAAATGGTAATTTTGGACTCTCGGGAGAAAAATGATAATTTTGGAAAAATTTAGGGTT
1 CGAGGGCAAAATGGTAATTTTAAACTCTCGAGAGAAAAATGATAATTTGGGAAAAATTTAGAGTT
* * * *
35366636 AAAAAATGATATTTTAGACACTTAAGGGTAAAATGGTAATTTTAAAAAGAATCAGGATCAAAACG
66 AAAAAATGACATTTTAAACACTTAAGGGTAAAACGGTAATTTTAAAAAGAATCAAGATCAAAACG
**
35366701 AGACTTTTTAGATGTT
131 AGACTTTTTAGACATT
*
35366717 CGAGGGCAAAATGGTAATTTTAAACTTTCGAGAGGAAAAATGATAATTTCGGGAAAAATTTAGAG
1 CGAGGGCAAAATGGTAATTTTAAACTCTCGAGA-GAAAAATGATAATTT-GGGAAAAATTTAGAG
* *
35366782 TT-AAAAATGACATTTTAAACACTTGAGGGTAAAACGGTAATTTTTAGAAA-AATCAAGATCAAA
64 TTAAAAAATGACATTTTAAACACTTAAGGGTAAAACGGTAA-TTTTAAAAAGAATCAAGATC-AA
* *
35366845 AATGAGA-TTTTTGGACATT
127 AACGAGACTTTTTAGACATT
* * *
35366864 CGGGGGTAAAATAGTAATTTT
1 CGAGGGCAAAATGGTAATTTT
35366885 GTGAATTTTG
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
146 28 0.19
147 85 0.59
148 31 0.22
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (146 bp):
CGAGGGCAAAATGGTAATTTTAAACTCTCGAGAGAAAAATGATAATTTGGGAAAAATTTAGAGTT
AAAAAATGACATTTTAAACACTTAAGGGTAAAACGGTAATTTTAAAAAGAATCAAGATCAAAACG
AGACTTTTTAGACATT
Found at i:35366915 original size:30 final size:29
Alignment explanation
Indices: 35366842--35367149 Score: 267
Period size: 29 Copynumber: 10.5 Consensus size: 29
35366832 AATCAAGATC
* *
35366842 AAAAATG-AGATTTTTGGACA-TTCGGGGGT
1 AAAAATGTA-ATTTTTGGA-ATTTTGAGGGT
35366871 -AAAATAGTAA-TTTTGTGAATTTTG-GGGT
1 AAAAAT-GTAATTTTTG-GAATTTTGAGGGT
* *
35366899 CAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 -AAAAATGTAATTTTTGGAATTTTGAGGGT
* *
35366929 AAAAATGTAATTTTTGGAAGTTCGAGGG-
1 AAAAATGTAATTTTTGGAATTTTGAGGGT
* *
35366957 AAAAATGTAATTTTAGAAAGTTTTG-GGGTT
1 AAAAATGTAATTTTTGGAA-TTTTGAGGG-T
*
35366987 AAAAATGTAATTTTTGGAAATTTGAGGGT
1 AAAAATGTAATTTTTGGAATTTTGAGGGT
* * *
35367016 AAAAATATAATTTTTGAAATTTTTAGGGTT
1 AAAAATGTAATTTTTGGAATTTTGAGGG-T
35367046 AAAAATGTAATTTTTGGAAGTTTTGAGGG-
1 AAAAATGTAATTTTTGGAA-TTTTGAGGGT
** *
35367075 AAAAATGTAATTTTTAAAACTTTT-AGGATT
1 AAAAATGTAATTTTTGGAA-TTTTGAGG-GT
*
35367105 AAAAATGTAATTTTGGAGAAGTTTTG-GGGT
1 AAAAATGTAATTTTTG-GAA-TTTTGAGGGT
* *
35367135 TAAAATATAATTTTT
1 AAAAATGTAATTTTT
35367150 AGATAGTTTA
Statistics
Matches: 230, Mismatches: 31, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
28 38 0.17
29 96 0.42
30 80 0.35
31 16 0.07
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAATTTTGAGGGT
Found at i:35367049 original size:59 final size:59
Alignment explanation
Indices: 35366871--35367162 Score: 303
Period size: 59 Copynumber: 4.9 Consensus size: 59
35366861 ATTCGGGGGT
* * * *
35366871 AAAATAGTAA-TTTTGTGAATTTTG-GGGTCAAAAATGGAATTTTTGGAAGTTTGAGGG-TA
1 AAAAT-GTAATTTTTG-GAAATTTGAGGGT-AAAAATGTAATTTTTGAAAGTTTTAGGGTTA
* * * *
35366930 AAAATGTAATTTTTGGAAGTTCGAGGG-AAAAATGTAATTTTAGAAAGTTTTGGGGTTA
1 AAAATGTAATTTTTGGAAATTTGAGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTTA
* *
35366988 AAAATGTAATTTTTGGAAATTTGAGGGTAAAAATATAATTTTTGAAATTTTTAGGGTTA
1 AAAATGTAATTTTTGGAAATTTGAGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTTA
* * * *
35367047 AAAATGTAATTTTTGGAAGTTTTGAGGG-AAAAATGTAATTTTTAAAACTTTTAGGATTA
1 AAAATGTAATTTTTGGAA-ATTTGAGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTTA
* * *
35367106 AAAATGTAA-TTTTGGAGAAGTTTTG-GGGTTAAAATATAATTTTTAGATAG-TTTAGGG
1 AAAATGTAATTTTTGGA-AA--TTTGAGGGTAAAAATGTAATTTTT-GAAAGTTTTAGGG
35367163 ACCTCTAAGG
Statistics
Matches: 198, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
57 23 0.12
58 44 0.22
59 98 0.49
60 31 0.16
61 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.39
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAATTTGAGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTTA
Found at i:35369117 original size:6 final size:6
Alignment explanation
Indices: 35369091--35369217 Score: 82
Period size: 6 Copynumber: 21.5 Consensus size: 6
35369081 TTTAAAAATT
* * *
35369091 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ATGA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** * * * *
35369138 AAATGA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA TTTTAGA A-ATAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA
* * * * *
35369185 ATTTAA AATTCA TTTTAA ACTTAA ATTAAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
35369218 GACCCAAAGT
Statistics
Matches: 88, Mismatches: 27, Indels: 11
0.70 0.21 0.09
Matches are distributed among these distances:
5 13 0.15
6 70 0.80
7 5 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:35369118 original size:17 final size:17
Alignment explanation
Indices: 35369091--35369156 Score: 96
Period size: 17 Copynumber: 3.8 Consensus size: 17
35369081 TTTAAAAATT
* *
35369091 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAATGA
35369109 ATTTAAATTTAAAATGA
1 ATTTAAATTTAAAATGA
35369126 ATTTAAATTTAAAAATGA
1 ATTTAAATTT-AAAATGA
35369144 ATTTAAATTTAAA
1 ATTTAAATTTAAA
35369157 TTTAAAGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 24 0.53
18 21 0.47
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATGA
Found at i:35369121 original size:35 final size:36
Alignment explanation
Indices: 35369075--35369156 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
35369065 TAATTTTAAT
* * *
35369075 TTTAATTTTAAAAAT-TATTTCAAATTT-AAACTAAA
1 TTTAAATTTAAAAATGAATTT-AAATTTAAAAATAAA
*
35369110 TTTAAATTT-AAAATGAATTTAAATTTAAAAATGAA
1 TTTAAATTTAAAAATGAATTTAAATTTAAAAATAAA
35369145 TTTAAATTTAAA
1 TTTAAATTTAAA
35369157 TTTAAAGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 11 0.28
35 27 0.68
36 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (36 bp):
TTTAAATTTAAAAATGAATTTAAATTTAAAAATAAA
Found at i:35369151 original size:41 final size:41
Alignment explanation
Indices: 35369106--35369191 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
35369096 AAATTTAAAC
* *
35369106 TAAATTTAAATTTAAAATGAATTTAAATTTAAAAATGAATT
1 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
* * *
35369147 TAAATTTAAATTTAAAGTAAATTTAATTTTAGAAATAAATT
1 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
35369188 TAAA
1 TAAA
35369192 ATTCATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (41 bp):
TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
Found at i:35369199 original size:24 final size:23
Alignment explanation
Indices: 35369172--35369217 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35369162 AGTAAATTTA
35369172 ATTTTAGAA-ATAAATTTAAAATTC
1 ATTTTA-AACATAAA-TTAAAATTC
*
35369196 ATTTTAAACTTAAATTAAAATT
1 ATTTTAAACATAAATTAAAATT
35369218 GACCCAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTTAAACATAAATTAAAATTC
Found at i:35369202 original size:41 final size:41
Alignment explanation
Indices: 35369106--35369217 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
35369096 AAATTTAAAC
* * *
35369106 TAAATTTAAATTTAAAATGAATTTAAATTTAAAAATGAATT
1 TAAAATTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
* * * *
35369147 TAAATTTAAATTTAAAGTAAATTTAATTTTAGAAATAAATT
1 TAAAATTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
* * * *
35369188 TAAAATTCATTTTAAACTTAAATTAAAATT
1 TAAAATTAAATTTAAA-ATAAATTTAAATT
35369218 GACCCAAAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
41 49 0.83
42 10 0.17
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (41 bp):
TAAAATTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
Found at i:35371794 original size:17 final size:17
Alignment explanation
Indices: 35371749--35371855 Score: 101
Period size: 17 Copynumber: 6.3 Consensus size: 17
35371739 CCCAAACCAT
* *
35371749 TTTAAATTTGCTTTGAAA
1 TTTAAATTT-ATTTTAAA
*
35371767 -TTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
35371783 TTCAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
35371800 TTTAAATTTATTTTTGA
1 TTTAAATTTATTTTAAA
*
35371817 TTTAAATTTAATTTT-AG
1 TTTAAATTT-ATTTTAAA
* *
35371834 TTTGAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
35371851 TTTAA
1 TTTAA
35371856 TATTATGGTA
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
16 10 0.14
17 57 0.79
18 5 0.07
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:35371800 original size:11 final size:11
Alignment explanation
Indices: 35371798--35371856 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
35371788 ATTTATTTTA
35371798 AATTTAAATTT
1 AATTTAAATTT
* **
35371809 ATTTTTGATTT
1 AATTTAAATTT
*
35371820 AAATTTAATTTT
1 -AATTTAAATTT
* *
35371832 AGTTTGAATTT
1 AATTTAAATTT
35371843 AATTTAAATTT
1 AATTTAAATTT
35371854 AAT
1 AAT
35371857 ATTATGGTAA
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
11 28 0.80
12 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:35371803 original size:6 final size:6
Alignment explanation
Indices: 35371777--35371855 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
35371767 TTAAGTTTAT
* * * **
35371777 TTTAAA TTCAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTGA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
35371823 TTT-AA TTTTAG TTTGAA TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
35371856 TATTATGGTA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
5 18 0.32
6 39 0.68
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:35371820 original size:23 final size:23
Alignment explanation
Indices: 35371794--35371854 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
35371784 TCAAATTTAT
*
35371794 TTTAAATTTAAATTTATTTTTG-A
1 TTTAAATTTAAATTTA-GTTTGAA
*
35371817 TTTAAATTTAATTTTAGTTTGAA
1 TTTAAATTTAAATTTAGTTTGAA
35371840 TTT-AATTTAAATTTA
1 TTTAAATTTAAATTTA
35371855 ATATTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTGAA
Found at i:35371869 original size:28 final size:28
Alignment explanation
Indices: 35371816--35371873 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
35371806 TTTATTTTTG
* * *
35371816 ATTTAAATTTAATTTTAGTTTGAATTTA
1 ATTTAAATTTAATATTAGTGTAAATTTA
35371844 ATTTAAATTTAATATTA-TGGTAAATTTA
1 ATTTAAATTTAATATTAGT-GTAAATTTA
35371872 AT
1 AT
35371874 GTCCATTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTTAAATTTAATATTAGTGTAAATTTA
Found at i:35373193 original size:30 final size:30
Alignment explanation
Indices: 35373136--35373193 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
35373126 TGACCGGTAT
*
35373136 GGAGGAAAGTTGAGAGAGTTTGAGAGAAGG
1 GGAGGAAAGTTGAGAGAGTTTCAGAGAAGG
* *
35373166 GGAGAGAAAGTT-TGAGAGTTTCTGAGAA
1 GGAG-GAAAGTTGAGAGAGTTTCAGAGAA
35373194 AAAGGAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.36, C:0.02, G:0.41, T:0.21
Consensus pattern (30 bp):
GGAGGAAAGTTGAGAGAGTTTCAGAGAAGG
Found at i:35373754 original size:29 final size:27
Alignment explanation
Indices: 35373721--35373921 Score: 86
Period size: 29 Copynumber: 6.9 Consensus size: 27
35373711 TCCCCAAGCT
35373721 TTCCAAAATTCCATTTTTAACCCCGAAAC
1 TTCCAAAATTCCA-TTTTAACCCCG-AAC
* **
35373750 TTCCAAAAATTATCATTTT-ACCCTTAAAC
1 TTCC-AAAATT-CCATTTTAACCC-CGAAC
* **
35373779 TTTCTAAAATTCCATTTTAACCCCG-GT
1 -TTCCAAAATTCCATTTTAACCCCGAAC
*
35373806 TTCACCAAAGATTACAATTTT-ACCCTCGAAC
1 TT--CCAAA-ATT-CCATTTTAACCC-CGAAC
* ** *
35373837 TTTCCAAAATCCCATTTTTAACCTTG-AT
1 -TTCCAAAATTCCA-TTTTAACCCCGAAC
*
35373865 TTCACCAAAAATTACCATTTTACCCCCGAATC
1 TT--CC-AAAATT-CCATTTTAACCCCGAA-C
*
35373897 TTCCAAAATCCCATTTTTAACCCCG
1 TTCCAAAATTCCA-TTTTAACCCCG
35373922 GTTTCACCAA
Statistics
Matches: 126, Mismatches: 25, Indels: 42
0.65 0.13 0.22
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 16 0.13
29 52 0.41
30 44 0.35
31 6 0.05
32 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (27 bp):
TTCCAAAATTCCATTTTAACCCCGAAC
Found at i:35373769 original size:30 final size:29
Alignment explanation
Indices: 35373721--35373803 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
35373711 TCCCCAAGCT
35373721 TTCC-AAAATTCCATTTTTAACCCCGAAAC
1 TTCCAAAAATTCCA-TTTTAACCCCGAAAC
* **
35373750 TTCCAAAAATTATCATTTT-ACCCTTAAAC
1 TTCCAAAAATT-CCATTTTAACCCCGAAAC
* *
35373779 TTTCTAAAATTCCATTTTAACCCCG
1 TTCCAAAAATTCCATTTTAACCCCG
35373804 GTTTCACCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.14
29 25 0.58
30 10 0.23
31 2 0.05
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTAACCCCGAAAC
Found at i:35373885 original size:59 final size:59
Alignment explanation
Indices: 35373719--35374068 Score: 422
Period size: 59 Copynumber: 5.9 Consensus size: 59
35373709 AGTCCCCAAG
* * * * *
35373719 CTTTCCAAAATTCCATTTTTAACCCCGAAACTT--CCAAAAATTATCATTTTACCCTTAAA
1 CTTTCCAAAATCCCATTTTTAACCTCG--ATTTCACCAAAAATTACCATTTTACCCTCAAA
* * * * * * *
35373778 CTTTCTAAAATTCCA-TTTTAACCCCGGTTTCACCAAAGATTACAATTTTACCCTCGAA
1 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAA
* * *
35373836 CTTTCCAAAATCCCATTTTTAACCTTGATTTCACCAAAAATTACCATTTTACCCCCGAA
1 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAA
* *
35373895 -TCTTCCAAAATCCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTACTCCT-AAA
1 CT-TTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTAC-CCTCAAA
*
35373954 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTTAAA
1 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTA-CCCTCAAA
* * **
35374014 CTTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAATTACGTTTTTACCCT
1 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCT
35374069 AGAATCTAAA
Statistics
Matches: 256, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
56 2 0.01
58 46 0.18
59 154 0.60
60 54 0.21
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAA
Found at i:35373931 original size:29 final size:28
Alignment explanation
Indices: 35373784--35373992 Score: 92
Period size: 29 Copynumber: 7.1 Consensus size: 28
35373774 TAAACTTTCT
* *
35373784 AAAATTCCATTTTAACCCCGGTTTCACC
1 AAAATCCCATTTTAACCCCGATTTCACC
* *
35373812 AAAGATTACAATTTT-ACCCTCGAACTTT--CC
1 AAA-A-TCCCATTTTAACCC-CG-A-TTTCACC
**
35373842 AAAATCCCATTTTTAACCTTGATTTCACC
1 AAAATCCCA-TTTTAACCCCGATTTCACC
* *
35373871 AAAAATTACCATTTTACCCCCGAATCTT--CC
1 -AAAA-TCCCATTTTAACCCCG-AT-TTCACC
*
35373901 AAAATCCCATTTTTAACCCCGGTTTCACC
1 AAAATCCCA-TTTTAACCCCGATTTCACC
* **
35373930 AAAAATTACCATTTT-ACTCCTAAACTTT--CC
1 -AAAA-TCCCATTTTAAC-CC-CGA-TTTCACC
*
35373960 AAAATCCCATTTTTAACCTCGATTTCACC
1 AAAATCCCA-TTTTAACCCCGATTTCACC
35373989 AAAA
1 AAAA
35373993 ATTACCATTT
Statistics
Matches: 134, Mismatches: 22, Indels: 49
0.65 0.11 0.24
Matches are distributed among these distances:
27 8 0.06
28 17 0.13
29 46 0.34
30 45 0.34
31 10 0.07
32 8 0.06
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATCCCATTTTAACCCCGATTTCACC
Found at i:35374050 original size:29 final size:28
Alignment explanation
Indices: 35373784--35374052 Score: 123
Period size: 30 Copynumber: 9.1 Consensus size: 28
35373774 TAAACTTTCT
* * *
35373784 AAAATTCCATTTTAACCCCGGTTTCACC
1 AAAATTCCATTTTAACCTCGATTTTACC
* * *
35373812 AAAGATTACAATTTTACCCTCGAACTTT-CC
1 AAA-ATT-CCATTTTAACCTCG-ATTTTACC
* * *
35373842 AAAATCCCATTTTTAACCTTGATTTCACC
1 AAAATTCCA-TTTTAACCTCGATTTTACC
* * *
35373871 AAAAATTACCATTTTACCCCCGAATCTT-CC
1 -AAAATT-CCATTTTAACCTCG-ATTTTACC
* * * *
35373901 AAAATCCCATTTTTAACCCCGGTTTCACC
1 AAAATTCCA-TTTTAACCTCGATTTTACC
* ** *
35373930 AAAAATTACCATTTTACTCCTAAACTTT-CC
1 -AAAATT-CCATTTTA-ACCTCGATTTTACC
* *
35373960 AAAATCCCATTTTTAACCTCGATTTCACC
1 AAAATTCCA-TTTTAACCTCGATTTTACC
* ** *
35373989 AAAAATTACCATTTTACCCCTTAAACTTT-CC
1 -AAAATT-CCATTTTA-ACC-TCGATTTTACC
35374020 AAAATTCCATTTTTAACCTCGATTTTACC
1 AAAATTCCA-TTTTAACCTCGATTTTACC
35374049 AAAA
1 AAAA
35374053 ATTACGTTTT
Statistics
Matches: 173, Mismatches: 47, Indels: 41
0.66 0.18 0.16
Matches are distributed among these distances:
28 27 0.16
29 56 0.32
30 64 0.37
31 22 0.13
32 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTCCATTTTAACCTCGATTTTACC
Found at i:35374089 original size:118 final size:119
Alignment explanation
Indices: 35373719--35374072 Score: 477
Period size: 118 Copynumber: 3.0 Consensus size: 119
35373709 AGTCCCCAAG
* * * *
35373719 CTTTCCAAAATTCCATTTTTAACCCCGAAACTT--CCAAAAATTATCATTTTA-CCCTTAAACTT
1 CTTTCCAAAATCCCATTTTTAACCTCG--ATTTCACCAAAAATTACCATTTTACCCCTTAAACTT
* * *
35373781 TCTAAAATTCCA-TTTTAACCCCGGTTTCACCAAAGATTACAATTTTACCCTCGAA
64 TCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACAATTTTACCCTAGAA
* ** *
35373836 CTTTCCAAAATCCCATTTTTAACCTTGATTTCACCAAAAATTACCATTTTACCCCCGAATC-TTC
1 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTTAAACTTTC
* *
35373900 CAAAATCCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTACTCCTA-AA
66 CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACAATTTTAC-CCTAGAA
35373954 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTTAAACTTTC
1 CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTTAAACTTTC
* * * **
35374019 CAAAATTCCATTTTTAACCTCGATTTTACCAAAAATTACGTTTTTACCCTAGAA
66 CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACAATTTTACCCTAGAA
35374073 TCTAAAAATT
Statistics
Matches: 207, Mismatches: 23, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
115 3 0.01
117 52 0.25
118 103 0.50
119 49 0.24
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (119 bp):
CTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTTAAACTTTC
CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACAATTTTACCCTAGAA
Found at i:35386750 original size:199 final size:200
Alignment explanation
Indices: 35386283--35386918 Score: 1008
Period size: 199 Copynumber: 3.2 Consensus size: 200
35386273 ACAAAACATT
*
35386283 GAGGCGGTCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* *
35386348 CTTCGAACCCAACTT-TCTGATGAGACACTGAGAAGCAGGTCGAAGGAATAAAATGGTTAGCTTC
66 CTTCGAACCCAGCTTCT-TGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* *
35386412 CTGATGAGATATAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATTCAGCGAAGCGAATCAAA
130 CTGATGAGATATAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAA
35386477 ACAAGC
195 ACAAGC
* * *
35386483 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACTAACTCAGCACTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
35386548 CTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* *
35386613 TAATGAGATACAGAGAAG-GGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
131 TGATGAGATATAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
35386677 CAAGC
196 CAAGC
* *
35386682 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* ** *
35386747 CTTCGAACCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCC
66 CTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * * *
35386812 TGATGAGACATAGAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCCAGAGAAGCGAATTAAAA
131 TGATGAGATATAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
*
35386877 C-AGAT
196 CAAG-C
* * *
35386882 GATTGCGGTCATCTTCCTGATAAGACACAGAGAAGAA
1 GA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAA
35386919 GACTAGGTCA
Statistics
Matches: 403, Mismatches: 29, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
199 187 0.46
200 184 0.46
201 32 0.08
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
CTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATATAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
CAAGC
Found at i:35387300 original size:17 final size:17
Alignment explanation
Indices: 35387255--35387361 Score: 101
Period size: 17 Copynumber: 6.3 Consensus size: 17
35387245 CCCAAACCAT
* *
35387255 TTTAAATTTGCTTTGAAA
1 TTTAAATTT-ATTTTAAA
*
35387273 -TTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
35387289 TTCAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
35387306 TTTAAATTTATTTTTGA
1 TTTAAATTTATTTTAAA
*
35387323 TTTAAATTTAATTTT-AG
1 TTTAAATTT-ATTTTAAA
* *
35387340 TTTGAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
35387357 TTTAA
1 TTTAA
35387362 TATTATGGTA
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
16 10 0.14
17 57 0.79
18 5 0.07
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:35387306 original size:11 final size:11
Alignment explanation
Indices: 35387304--35387362 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
35387294 ATTTATTTTA
35387304 AATTTAAATTT
1 AATTTAAATTT
* **
35387315 ATTTTTGATTT
1 AATTTAAATTT
*
35387326 AAATTTAATTTT
1 -AATTTAAATTT
* *
35387338 AGTTTGAATTT
1 AATTTAAATTT
35387349 AATTTAAATTT
1 AATTTAAATTT
35387360 AAT
1 AAT
35387363 ATTATGGTAA
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
11 28 0.80
12 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:35387309 original size:6 final size:6
Alignment explanation
Indices: 35387283--35387361 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
35387273 TTAAGTTTAT
* * * **
35387283 TTTAAA TTCAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTGA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
35387329 TTT-AA TTTTAG TTTGAA TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
35387362 TATTATGGTA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
5 18 0.32
6 39 0.68
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:35387326 original size:23 final size:23
Alignment explanation
Indices: 35387300--35387360 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
35387290 TCAAATTTAT
*
35387300 TTTAAATTTAAATTTATTTTTG-A
1 TTTAAATTTAAATTTA-GTTTGAA
*
35387323 TTTAAATTTAATTTTAGTTTGAA
1 TTTAAATTTAAATTTAGTTTGAA
35387346 TTT-AATTTAAATTTA
1 TTTAAATTTAAATTTA
35387361 ATATTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTGAA
Found at i:35387375 original size:28 final size:28
Alignment explanation
Indices: 35387322--35387379 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
35387312 TTTATTTTTG
* * *
35387322 ATTTAAATTTAATTTTAGTTTGAATTTA
1 ATTTAAATTTAATATTAGTGTAAATTTA
35387350 ATTTAAATTTAATATTA-TGGTAAATTTA
1 ATTTAAATTTAATATTAGT-GTAAATTTA
35387378 AT
1 AT
35387380 GTCCATTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTTAAATTTAATATTAGTGTAAATTTA
Found at i:35388100 original size:16 final size:16
Alignment explanation
Indices: 35388069--35388112 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
35388059 ATTAATAGTA
*
35388069 ATTAATAAATATATTTAT
1 ATTAAT-AATAAATTT-T
35388087 ATT-ATAATAAATTTT
1 ATTAATAATAAATTTT
35388102 ATTAATAATAA
1 ATTAATAATAA
35388113 TATTAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 2 0.08
18 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAATAATAAATTTT
Found at i:35388446 original size:18 final size:18
Alignment explanation
Indices: 35388423--35388457 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35388413 TTAAAATGCT
35388423 CAGATCTGGTTCAAAAAC
1 CAGATCTGGTTCAAAAAC
*
35388441 CAGATCTGGTTTAAAAA
1 CAGATCTGGTTCAAAAA
35388458 TGAAACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (18 bp):
CAGATCTGGTTCAAAAAC
Found at i:35389328 original size:59 final size:59
Alignment explanation
Indices: 35389232--35389664 Score: 541
Period size: 59 Copynumber: 7.3 Consensus size: 59
35389222 AGTCCCCAAG
* * * * *
35389232 CTTTCCAAAATTCCATTTTTAACCTCGAAACTT--CCAAAAATTACGATTTTACCCTTAAA
1 CTTTCCAAAATCCCATTTTTAACC-C-CAATTTCACCAAAAATTACCATTTTACCCCTAAA
* ** ** **
35389291 CTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAGGTTACCATTTTACCCCCGAA
1 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAA
* * *
35389350 CTTTCCAAAATCCCATTTTTAACCTCAAGTTCACTAAAAATTACCATTTTACCCCTAAA
1 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAA
* * * **
35389409 CTTTCCAAAATCTCATTTTTAACCTCAGTTTCACCAAAAATTACCATTTTACCCCCGAA
1 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAA
** * *
35389468 -TCTTCCAAAATCCCATTTTTAACCCCGGTTTCAGCAAAAATTACCATTTTACCCTTAAA
1 CT-TTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAA
* * *
35389527 CTTTCTAAAATCCCA-TTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCTAAA
1 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAA
*
35389585 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTATCATTTTACCCCCTAAA
1 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTA-CCCCTAAA
*
35389645 CTTTCCAAAATTCCATTTTT
1 CTTTCCAAAATCCCATTTTT
35389665 TGACCTTGAT
Statistics
Matches: 323, Mismatches: 45, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
57 2 0.01
58 53 0.16
59 240 0.74
60 28 0.09
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAA
Found at i:35389531 original size:177 final size:177
Alignment explanation
Indices: 35389232--35389664 Score: 599
Period size: 177 Copynumber: 2.5 Consensus size: 177
35389222 AGTCCCCAAG
* * *
35389232 CTTTCCAAAAT-TCCATTTTTAACCTCGAAACTT--CCAAAAATTACGATTTTA-CCCTTAAACT
1 CTTTCCAAAATCT-CATTTTTAACCTC--AATTTCACCAAAAATTACCATTTTACCCCCTAAACT
** *
35389293 TTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAGGTTACCATTTTACCCCCGAACTTTCCAA
63 TTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAA
*
35389358 AATCCCATTTTTAA-CCTCAAGTTCACTAAAAATTACCATTTTACCCCTAAA
128 AATCCCA-TTTTAACCCT-AAGTTCACCAAAAATTACCATTTTACCCCTAAA
* * *
35389409 CTTTCCAAAATCTCATTTTTAACCTCAGTTTCACCAAAAATTACCATTTTACCCCCGAATC-TTC
1 CTTTCCAAAATCTCATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCTAAACTTTC
* * ** *
35389473 CAAAATCCCATTTTTAACCCCGGTTTCAGCAAAAATTACCATTTTACCCTTAAACTTTCTAAAAT
66 CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
* *
35389538 CCCATTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCTAAA
131 CCCATTTTAACCCTAAGTTCACCAAAAATTACCATTTTACCCCTAAA
* * *
35389585 CTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTATCATTTTACCCCCTAAACTTTC
1 CTTTCCAAAATCTCATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCTAAACTTTC
35389650 CAAAATTCCATTTTT
66 CAAAATTCCATTTTT
35389665 TGACCTTGAT
Statistics
Matches: 226, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
175 3 0.01
176 91 0.40
177 125 0.55
178 7 0.03
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (177 bp):
CTTTCCAAAATCTCATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCTAAACTTTC
CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
CCCATTTTAACCCTAAGTTCACCAAAAATTACCATTTTACCCCTAAA
Found at i:35389655 original size:30 final size:29
Alignment explanation
Indices: 35389232--35389663 Score: 158
Period size: 30 Copynumber: 14.7 Consensus size: 29
35389222 AGTCCCCAAG
* *
35389232 CTTTCCAAAATT-CCATTTTTAACCTCGAAA
1 CTTTCCAAAATTACCA-TTTT-ACCCCTAAA
* *
35389262 C-TTCCAAAAATTACGATTTTACCCTTAAA
1 CTTTCC-AAAATTACCATTTTACCCCTAAA
*
35389291 CTTTCCAAAATT-CCATTTTTAACCCC---G
1 CTTTCCAAAATTACCA-TTTT-ACCCCTAAA
* * **
35389318 GTTTCACCAAAGGTTACCATTTTACCCCCGAA
1 CTTT--CCAAA-ATTACCATTTTACCCCTAAA
* * *
35389350 CTTTCCAAAA-TCCCATTTTTA-ACCTCAA
1 CTTTCCAAAATTACCA-TTTTACCCCTAAA
*
35389378 -GTTCACTAAAAATTACCATTTTACCCCTAAA
1 CTTTC-C--AAAATTACCATTTTACCCCTAAA
* *
35389409 CTTTCCAAAA-T-CTCATTTTTA-ACCT-CA
1 CTTTCCAAAATTAC-CA-TTTTACCCCTAAA
* **
35389436 GTTTCACCAAAAATTACCATTTTACCCCCGAA
1 CTTT--CC-AAAATTACCATTTTACCCCTAAA
* *
35389468 -TCTTCCAAAA-TCCCATTTTTAACCCC---G
1 CT-TTCCAAAATTACCA-TTTT-ACCCCTAAA
* *
35389495 GTTTCAGCAAAAATTACCATTTTACCCTTAAA
1 CTTTC--C-AAAATTACCATTTTACCCCTAAA
* * *
35389527 CTTTCTAAAA-TCCCATTTTAACCCT-AA
1 CTTTCCAAAATTACCATTTTACCCCTAAA
*
35389554 TTTTACCAAAAATTACCATTTTACCCCTAAA
1 CTTT-CC-AAAATTACCATTTTACCCCTAAA
*
35389585 CTTTCCAAAA-TCCCATTTTTAACCCC--AA
1 CTTTCCAAAATTACCA-TTTT-ACCCCTAAA
*
35389613 -TTTCACCAAAAATTATCATTTTACCCCCTAAA
1 CTTT--CC-AAAATTACCATTTTA-CCCCTAAA
35389645 CTTTCCAAAATT-CCATTTT
1 CTTTCCAAAATTACCATTTT
35389664 TTGACCTTGA
Statistics
Matches: 303, Mismatches: 46, Indels: 107
0.66 0.10 0.23
Matches are distributed among these distances:
27 22 0.07
28 41 0.14
29 85 0.28
30 101 0.33
31 35 0.12
32 16 0.05
33 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
CTTTCCAAAATTACCATTTTACCCCTAAA
Found at i:35395069 original size:26 final size:27
Alignment explanation
Indices: 35395020--35395080 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
35395010 TGGAGCTTGT
* *
35395020 TGACGTGGCCTGTGATGACGTGGTAAC
1 TGACGTGGACTGTGATGACATGGTAAC
* *
35395047 TGACGTGGAC-GTGCTGACATGGTAGC
1 TGACGTGGACTGTGATGACATGGTAAC
*
35395073 TGATGTGG
1 TGACGTGG
35395081 CGGCTTAGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.26
Consensus pattern (27 bp):
TGACGTGGACTGTGATGACATGGTAAC
Found at i:35395218 original size:17 final size:17
Alignment explanation
Indices: 35395196--35395281 Score: 93
Period size: 17 Copynumber: 5.1 Consensus size: 17
35395186 ATTAAACTTT
35395196 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
35395213 TAAATTTAAACTTCAAA
1 TAAATTTAAATTTAAAA
** *
35395230 TAAGCTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
35395247 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
*
35395264 TGAA-TTAAGATTTAAAA
1 TAAATTTAA-ATTTAAAA
35395281 T
1 T
35395282 CTAAAGTTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
16 4 0.07
17 51 0.93
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:35397208 original size:31 final size:29
Alignment explanation
Indices: 35397128--35397184 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
35397118 GAATTAGGTC
*
35397128 AAATCAAAATTTCATATATAAAATTGCATA
1 AAATCAAAA-TTCATATATAAAATTACATA
*
35397158 AAATCAAAATTCATTTATAAAATTACA
1 AAATCAAAATTCATATATAAAATTACA
35397185 CATTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (29 bp):
AAATCAAAATTCATATATAAAATTACATA
Found at i:35402295 original size:55 final size:55
Alignment explanation
Indices: 35402234--35402343 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
35402224 ATTATTTCTA
*
35402234 GATTAGTTACATTATTATTCAAATAGTTTCTATTTCA-CTATTTTAAAAGTCAAAT
1 GATTAGTTACATTATTATTCAAATAGTCTCTATTTCATC-ATTTTAAAAGTCAAAT
35402289 GATTAGTTACATTATTATTCAAATAGTCTCTATTTCATCATTTTAAAAGTCAAAT
1 GATTAGTTACATTATTATTCAAATAGTCTCTATTTCATCATTTTAAAAGTCAAAT
35402344 TTCAAAGGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (55 bp):
GATTAGTTACATTATTATTCAAATAGTCTCTATTTCATCATTTTAAAAGTCAAAT
Found at i:35406931 original size:21 final size:21
Alignment explanation
Indices: 35406907--35406953 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
35406897 TATGTTTCAC
35406907 AATTGTGTTAATAAT-T-TCTTA
1 AATTGTG-TAA-AATATATCTTA
*
35406928 AATTATGTAAAATATATCTTA
1 AATTGTGTAAAATATATCTTA
35406949 AATTG
1 AATTG
35406954 AAACATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (21 bp):
AATTGTGTAAAATATATCTTA
Found at i:35411187 original size:4 final size:4
Alignment explanation
Indices: 35411165--35411206 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
35411155 GGTTTGTATA
* *
35411165 TATT TATT AATT T-TAT TATT TATT TATT TGTT TATT TATT TA
1 TATT TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TA
35411207 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 1 0.03
4 30 0.94
5 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:35411205 original size:16 final size:16
Alignment explanation
Indices: 35411165--35411206 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
35411155 GGTTTGTATA
*
35411165 TATTTATTAATTTTAT
1 TATTTATTTATTTTAT
35411181 TATTTATTTATTTGT-T
1 TATTTATTTATTT-TAT
35411197 TATTTATTTA
1 TATTTATTTA
35411207 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTTTAT
Found at i:35411221 original size:11 final size:11
Alignment explanation
Indices: 35411205--35411229 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35411195 TTTATTTATT
35411205 TAATAAATAAA
1 TAATAAATAAA
35411216 TAATAAATAAA
1 TAATAAATAAA
35411227 TAA
1 TAA
35411230 AATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:35411819 original size:39 final size:39
Alignment explanation
Indices: 35411763--35411906 Score: 146
Period size: 39 Copynumber: 3.6 Consensus size: 39
35411753 GTTTCAACTC
* *
35411763 GCCCCATGGTCGGGGTAAGAGATTGGATTTCTTTAATAT
1 GCCCCATGATCGGGGTAAAAGATTGGATTTCTTTAATAT
* * * *
35411802 GCCCCATGATCGAGGTAAAAGATCGGATGGTCTTTAATCTT
1 GCCCCATGATCGGGGTAAAAGATTGGAT-TTCTTTAAT-AT
* * ** *
35411843 G-CCCTTTAGTTAGGGTAAAAGATTGGATTTCTTTAATCT
1 GCCCCATGA-TCGGGGTAAAAGATTGGATTTCTTTAATAT
*
35411882 GCCCCATGATCGGGGTAAAATATTG
1 GCCCCATGATCGGGGTAAAAGATTG
35411907 AAGGTTGTTA
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
39 39 0.48
40 26 0.32
41 17 0.21
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
GCCCCATGATCGGGGTAAAAGATTGGATTTCTTTAATAT
Found at i:35412117 original size:99 final size:100
Alignment explanation
Indices: 35411963--35412187 Score: 335
Period size: 99 Copynumber: 2.3 Consensus size: 100
35411953 TCATTGTGAC
* * * * * *
35411963 TTCAATCTTCCCCTCTACAGCTTTAGGTTAATGAGATTTGTCATTACGGCTTCATTCTGTCCCTC
1 TTCAATCTGCACCTCTATAGCTTTAGGTGAATGAGATTTGCCATTACGGCTTCATTCTGCCCCTC
* * *
35412028 TACATCTTTTGGT-TATGAGATTTGCCTTTGCAGT
66 TACAGCTTTAGCTGTATGAGATTTGCCTTTGCAGT
* *
35412062 TTCAGTCTGCACCTCTATAGCTTTAGGTGAATGAGATTTGCCATTGCGGCTTCATTCTGCCCCTC
1 TTCAATCTGCACCTCTATAGCTTTAGGTGAATGAGATTTGCCATTACGGCTTCATTCTGCCCCTC
*
35412127 TACAGCTTTAGCTGTATGAGATTTGCCTTTGCGGT
66 TACAGCTTTAGCTGTATGAGATTTGCCTTTGCAGT
35412162 TTCAATCTGCACCTCTATAGCTTTAG
1 TTCAATCTGCACCTCTATAGCTTTAG
35412188 CGGTAAAAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 67 0.60
100 45 0.40
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (100 bp):
TTCAATCTGCACCTCTATAGCTTTAGGTGAATGAGATTTGCCATTACGGCTTCATTCTGCCCCTC
TACAGCTTTAGCTGTATGAGATTTGCCTTTGCAGT
Found at i:35412188 original size:50 final size:49
Alignment explanation
Indices: 35411962--35412187 Score: 238
Period size: 50 Copynumber: 4.6 Consensus size: 49
35411952 GTCATTGTGA
* * * *
35411962 CTTCAATCTTCCCCTCTACAGCTTTAGGTTAATGAGATTTGTCATTACGG
1 CTTCAATCTGCACCTCTACAGCTTTAGGTT-ATGAGATTTGCCATTGCGG
* * * * *
35412012 CTTCATTCTGTC-CCTCTACATCTTTTGGTTATGAGATTTGCCTTTGCAG
1 CTTCAATCTG-CACCTCTACAGCTTTAGGTTATGAGATTTGCCATTGCGG
* * * *
35412061 TTTCAGTCTGCACCTCTATAGCTTTAGGTGAATGAGATTTGCCATTGCGG
1 CTTCAATCTGCACCTCTACAGCTTTAGGT-TATGAGATTTGCCATTGCGG
* * * *
35412111 CTTCATTCTGCCCCTCTACAGCTTTAGCTGTATGAGATTTGCCTTTGCGG
1 CTTCAATCTGCACCTCTACAGCTTTAGGT-TATGAGATTTGCCATTGCGG
* *
35412161 TTTCAATCTGCACCTCTATAGCTTTAG
1 CTTCAATCTGCACCTCTACAGCTTTAG
35412188 CGGTAAAAGA
Statistics
Matches: 146, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.01
49 37 0.25
50 107 0.73
51 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (49 bp):
CTTCAATCTGCACCTCTACAGCTTTAGGTTATGAGATTTGCCATTGCGG
Found at i:35420322 original size:8 final size:8
Alignment explanation
Indices: 35420303--35420341 Score: 69
Period size: 8 Copynumber: 4.8 Consensus size: 8
35420293 AATGTATGAA
35420303 AATGCAATG
1 AATGC-ATG
35420312 AATGCATG
1 AATGCATG
35420320 AATGCATG
1 AATGCATG
35420328 AATGCATG
1 AATGCATG
35420336 AATGCA
1 AATGCA
35420342 AATGCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 25 0.83
9 5 0.17
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (8 bp):
AATGCATG
Found at i:35423042 original size:16 final size:18
Alignment explanation
Indices: 35423008--35423043 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35422998 AACATGTTAT
35423008 AATCACAACAAACATATA
1 AATCACAACAAACATATA
35423026 AATCACAA-AAA-ATATA
1 AATCACAACAAACATATA
35423042 AA
1 AA
35423044 ATAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
AATCACAACAAACATATA
Found at i:35424965 original size:16 final size:16
Alignment explanation
Indices: 35424937--35424978 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
35424927 GGTTTGTATA
*
35424937 TATTTATTAATTT-TAT
1 TATTTATTTATTTGT-T
*
35424953 TATTTCTTTATTTGTT
1 TATTTATTTATTTGTT
35424969 TATTTATTTA
1 TATTTATTTA
35424979 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTTGTT
Found at i:35428443 original size:14 final size:15
Alignment explanation
Indices: 35428380--35428445 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
35428370 TTAATTTTTT
*
35428380 TAAATTTTTTAATAA
1 TAAATATTTTAATAA
*
35428395 TATATATTTTATATACA
1 TAAATATTTTA-ATA-A
* * *
35428412 TAGATATTTGAAT-C
1 TAAATATTTTAATAA
35428426 TAAATATTTTAA-AA
1 TAAATATTTTAATAA
35428440 TAAATA
1 TAAATA
35428446 ATATTCTCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
14 16 0.40
15 9 0.22
16 5 0.12
17 10 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
TAAATATTTTAATAA
Found at i:35433081 original size:23 final size:23
Alignment explanation
Indices: 35433007--35433197 Score: 105
Period size: 23 Copynumber: 8.5 Consensus size: 23
35432997 TAAACGGAAC
* * *
35433007 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
35433029 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
35433051 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
35433077 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
35433097 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
35433116 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
35433139 AATAATAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
* * *
35433164 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
35433187 AATCAGAGAGC
1 AAACAGAGAGC
35433198 GCGCTAGTGT
Statistics
Matches: 128, Mismatches: 25, Indels: 31
0.70 0.14 0.17
Matches are distributed among these distances:
16 10 0.08
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 18 0.14
23 55 0.43
24 2 0.02
25 28 0.22
26 8 0.06
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:35433148 original size:25 final size:23
Alignment explanation
Indices: 35433100--35433197 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
35433090 ACAAAGTACT
*
35433100 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
*
35433123 GAGCACACACAGTGCTAATAATAGA
1 GAGCACACACAGTGCTAAT--CAGA
* *
35433148 GAGCACGAGAC-GTGCTAATCGGA
1 GAGCAC-ACACAGTGCTAATCAGA
35433171 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
35433194 GAGC
1 GAGC
35433198 GCGCTAGTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
22 3 0.05
23 41 0.64
25 17 0.27
26 3 0.05
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:35434281 original size:33 final size:36
Alignment explanation
Indices: 35434220--35434285 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
35434210 CTCTTTTACC
* *
35434220 CCTTGCTCTACTCTTTTCCTTTGTCTTCAATTTGAT
1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT
35434256 CCTTGC-CT-CTCTTCT-CTTTCTCTTCAATTT
1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTT
35434286 CACATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.50
34 6 0.21
35 2 0.07
36 6 0.21
ACGTcount: A:0.09, C:0.32, G:0.06, T:0.53
Consensus pattern (36 bp):
CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT
Found at i:35436182 original size:21 final size:22
Alignment explanation
Indices: 35436132--35436182 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
35436122 AATTATAAAA
*
35436132 TTTAAAA-ATATTTTAAAGGTT
1 TTTAAAATATATTTTAAAGCTT
* *
35436153 TTTGTAAATATATTTTATA-CTT
1 TTT-AAAATATATTTTAAAGCTT
35436175 TTTAAAAT
1 TTTAAAAT
35436183 TAAAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 7 0.29
22 8 0.33
23 9 0.38
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTAAAATATATTTTAAAGCTT
Found at i:35436831 original size:12 final size:11
Alignment explanation
Indices: 35436789--35436852 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
35436779 TTTTACTTTG
*
35436789 AAATTAAATTT
1 AAATTAATTTT
*
35436800 -ATTTAATTTT
1 AAATTAATTTT
*
35436810 AAATTTATTTT
1 AAATTAATTTT
35436821 AAATTCAATTTT
1 AAATT-AATTTT
*
35436833 AATTTTAATTTT
1 AA-ATTAATTTT
*
35436845 AATTTAAT
1 AAATTAAT
35436853 ATTATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
10 8 0.18
11 19 0.43
12 15 0.34
13 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
AAATTAATTTT
Found at i:35436851 original size:11 final size:12
Alignment explanation
Indices: 35436800--35436852 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
35436790 AATTAAATTT
35436800 ATTTAATTTTAA
1 ATTTAATTTTAA
35436812 ATTT-ATTTTAA
1 ATTTAATTTTAA
*
35436823 ATTCAATTTTAA
1 ATTTAATTTTAA
*
35436835 TTTTAATTTT-A
1 ATTTAATTTTAA
35436846 ATTTAAT
1 ATTTAAT
35436853 ATTATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 17 0.47
12 19 0.53
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTAATTTTAA
Found at i:35438158 original size:18 final size:19
Alignment explanation
Indices: 35438132--35438174 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
35438122 AGATGCAAAG
35438132 GAAAAGAAGAAAGAGAT-A
1 GAAAAGAAGAAAGAGATAA
* **
35438150 GAAAGGAAGCGAGAGATAA
1 GAAAAGAAGAAAGAGATAA
35438169 GAAAAG
1 GAAAAG
35438175 CCCGACAGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.05
Consensus pattern (19 bp):
GAAAAGAAGAAAGAGATAA
Found at i:35441691 original size:23 final size:23
Alignment explanation
Indices: 35441665--35441827 Score: 153
Period size: 23 Copynumber: 7.3 Consensus size: 23
35441655 AGTGCTGGGC
35441665 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
35441688 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
35441707 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
35441727 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
35441750 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
35441774 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
35441798 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
35441821 ATCAGAG
1 AACAGAG
35441828 CGCGCGCTAG
Statistics
Matches: 113, Mismatches: 16, Indels: 22
0.75 0.11 0.15
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 76 0.67
24 2 0.02
25 16 0.14
26 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:35441725 original size:39 final size:39
Alignment explanation
Indices: 35441671--35441745 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
35441661 GGGCAACAGA
*
35441671 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
35441710 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
35441746 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:35441784 original size:48 final size:46
Alignment explanation
Indices: 35441710--35441827 Score: 175
Period size: 48 Copynumber: 2.5 Consensus size: 46
35441700 ACAAAGTACT
* *
35441710 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
35441756 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
35441804 GAGCACACACAGTGCTAATCAGAG
1 GAGCACACACAGTGCTAATCAGAG
35441828 CGCGCGCTAG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 23 0.35
48 42 0.64
49 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:35448126 original size:23 final size:23
Alignment explanation
Indices: 35448100--35448262 Score: 153
Period size: 23 Copynumber: 7.3 Consensus size: 23
35448090 AGTGCTGGGC
35448100 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
35448123 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
35448142 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
35448162 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
35448185 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
35448209 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
35448233 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
35448256 ATCAGAG
1 AACAGAG
35448263 TGCGCGCTAG
Statistics
Matches: 113, Mismatches: 16, Indels: 22
0.75 0.11 0.15
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 76 0.67
24 2 0.02
25 16 0.14
26 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:35448160 original size:39 final size:39
Alignment explanation
Indices: 35448106--35448180 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
35448096 GGGCAACAGA
*
35448106 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
35448145 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
35448181 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:35448219 original size:48 final size:46
Alignment explanation
Indices: 35448145--35448262 Score: 175
Period size: 48 Copynumber: 2.5 Consensus size: 46
35448135 ACAAAGTACT
* *
35448145 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
35448191 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
35448239 GAGCACACACAGTGCTAATCAGAG
1 GAGCACACACAGTGCTAATCAGAG
35448263 TGCGCGCTAG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 23 0.35
48 42 0.64
49 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:35452433 original size:92 final size:92
Alignment explanation
Indices: 35452266--35452543 Score: 475
Period size: 92 Copynumber: 3.0 Consensus size: 92
35452256 TTAGATCAAA
* *
35452266 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAAAATCAACTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
* *
35452331 ATTCTCTTGAATTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
35452358 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGTTTCAAACATCAATTCTT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
*
35452423 ATCCTTTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
35452450 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAATAAGAGCAAGATGAAGTTTCAAACACCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
35452515 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
35452542 AT
1 AT
35452544 TTGAAATGAA
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 174 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (92 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGTAGTAAAGTTGG
Found at i:35452746 original size:22 final size:22
Alignment explanation
Indices: 35452721--35452787 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
35452711 CCCAAACCAT
*
35452721 TTTTACTTTGAAATTAAATTTA
1 TTTTAATTTGAAATTAAATTTA
* *
35452743 TTTTAATTTTAAATTTAATTTAAA
1 TTTTAATTTGAAATTAAATTT--A
* *
35452767 TTTAAATTTG-AATTTAATTTA
1 TTTTAATTTGAAATTAAATTTA
35452788 AATTTAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 18 0.47
23 10 0.26
24 9 0.24
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTAATTTGAAATTAAATTTA
Found at i:35452770 original size:23 final size:23
Alignment explanation
Indices: 35452722--35452795 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
35452712 CCAAACCATT
* * * *
35452722 TTTACTTTGAAATTAAATTT-AT
1 TTTAATTTTAAATTTAATTTAAA
35452744 TTTAATTTTAAATTTAATTTAAA
1 TTTAATTTTAAATTTAATTTAAA
* *
35452767 TTTAAATTTGAATTTAATTTAAA
1 TTTAATTTTAAATTTAATTTAAA
35452790 TTTAAT
1 TTTAAT
35452796 ATTATTATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 17 0.39
23 27 0.61
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTAATTTTAAATTTAATTTAAA
Found at i:35452793 original size:6 final size:6
Alignment explanation
Indices: 35452734--35452794 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
35452724 TACTTTGAAA
* * *
35452734 TTAAAT TT-ATT TTAATT TTAAAT TT-AAT TTAAAT TTAAAT TTGAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
35452780 TT-AAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAA
35452795 TATTATTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
5 14 0.29
6 35 0.71
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:35452813 original size:17 final size:16
Alignment explanation
Indices: 35452734--35452812 Score: 97
Period size: 17 Copynumber: 4.7 Consensus size: 16
35452724 TACTTTGAAA
*
35452734 TTAAATTTATTTTAATT
1 TTAAATTTAATTTAA-T
35452751 TTAAATTTAATTTAAAT
1 TTAAATTTAATTT-AAT
35452768 TTAAATTTGAATTTAAT
1 TTAAATTT-AATTTAAT
35452785 TTAAATTTAATATT-AT
1 TTAAATTTAAT-TTAAT
35452801 TATAAATTTAAT
1 T-TAAATTTAAT
35452813 AAAATGTCCA
Statistics
Matches: 57, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
16 6 0.11
17 44 0.77
18 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TTAAATTTAATTTAAT
Found at i:35453269 original size:43 final size:44
Alignment explanation
Indices: 35453221--35453315 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
35453211 TTCATTGTAA
* * *
35453221 TAAAAAAA-CCCAGTTTTGGAAATCAATAGATATACCCTGTTCT
1 TAAAAAAACCCCAATTCTGAAAATCAATAGATATACCCTGTTCT
35453264 TAAAAAAACCCCAATTCTGAAAATCAATAGATATACCCTGTTCT
1 TAAAAAAACCCCAATTCTGAAAATCAATAGATATACCCTGTTCT
35453308 TAAAAAAA
1 TAAAAAAA
35453316 ACCCTCTTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 8 0.17
44 40 0.83
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.27
Consensus pattern (44 bp):
TAAAAAAACCCCAATTCTGAAAATCAATAGATATACCCTGTTCT
Found at i:35453656 original size:21 final size:20
Alignment explanation
Indices: 35453625--35453666 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
35453615 TTAATAGTAA
*
35453625 ATAATAATATTATTTATAAT
1 ATAATAATATTATTAATAAT
35453645 ATAATAAATATTATTAATAAT
1 ATAAT-AATATTATTAATAAT
35453666 A
1 A
35453667 ATATTAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATAATATTATTAATAAT
Found at i:35453672 original size:12 final size:12
Alignment explanation
Indices: 35453624--35453672 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
35453614 ATTAATAGTA
35453624 AATAATAATATT
1 AATAATAATATT
* *
35453636 ATTTATAATA-T
1 AATAATAATATT
*
35453647 AATAAATATTATT
1 AAT-AATAATATT
35453660 AATAATAATATT
1 AATAATAATATT
35453672 A
1 A
35453673 GTAAAAACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
11 3 0.10
12 22 0.76
13 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATAATAATATT
Found at i:35453750 original size:17 final size:19
Alignment explanation
Indices: 35453728--35453770 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
35453718 CGGTAATAGT
35453728 AATAATA-AA-TATTAATA
1 AATAATATAATTATTAATA
35453745 AATAATATTAATTTATTAATA
1 AATAATA-TAA-TTATTAATA
35453766 AATAA
1 AATAA
35453771 AAAAAGGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
19 2 0.09
21 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATATAATTATTAATA
Found at i:35454975 original size:31 final size:30
Alignment explanation
Indices: 35454905--35455088 Score: 137
Period size: 30 Copynumber: 6.1 Consensus size: 30
35454895 ACTTTGAAGG
* * *
35454905 ACCCTA-AACTATCCAAAAATGATATTTTGA
1 ACCCTAGAACT-TCCAAAAATTACATTTTTA
*
35454935 CCCCT-GAACTTCTTC-AAAATTACATTTTTA
1 ACCCTAGAACTTC--CAAAAATTACATTTTTA
* * * *
35454965 ACCTTCGAACTTCCAAAAATTCCATTTTTG
1 ACCCTAGAACTTCCAAAAATTACATTTTTA
* *
35454995 ACCCTAAAACTTCCAAAAATTACATTTTTGC
1 ACCCTAGAACTTCCAAAAATTACATTTTT-A
* *
35455026 ACCC-A-AACTTCCAAAAATTTCATTTTTTTG
1 ACCCTAGAACTTCCAAAAATTACA--TTTTTA
* * *
35455056 A-CCTCGAACTTCCAAAACTTCCATTTTTA
1 ACCCTAGAACTTCCAAAAATTACATTTTTA
35455085 ACCC
1 ACCC
35455089 CAAAACTCTT
Statistics
Matches: 124, Mismatches: 19, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
29 27 0.22
30 65 0.52
31 32 0.26
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (30 bp):
ACCCTAGAACTTCCAAAAATTACATTTTTA
Found at i:35455014 original size:90 final size:90
Alignment explanation
Indices: 35454904--35455095 Score: 216
Period size: 90 Copynumber: 2.1 Consensus size: 90
35454894 TACTTTGAAG
* *
35454904 GACCCT-AAACTATCCAAAAATGATA-TTTTG-ACCCCTGAACTTCTTC-AAAATTACA-TTTTT
1 GACCCTAAAACTATCCAAAAATGACATTTTTGCA-CCC-AAACTTC--CAAAAATTACATTTTTT
35454964 AACCTTCGAACTTCCAAAAATTCCATTTTT
62 AACC-TCGAACTTCCAAAAATTCCATTTTT
* * *
35454994 GACCCTAAAACT-TCCAAAAATTACATTTTTGCACCCAAACTTCCAAAAATTTCATTTTTTTGAC
1 GACCCTAAAACTATCCAAAAATGACATTTTTGCACCCAAACTTCCAAAAATTACA-TTTTTTAAC
*
35455058 CTCGAACTTCCAAAACTTCCATTTTT
65 CTCGAACTTCCAAAAATTCCATTTTT
* *
35455084 AACCCCAAAACT
1 GACCCTAAAACT
35455096 CTTAAAATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
88 1 0.01
89 8 0.09
90 57 0.65
91 21 0.24
92 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (90 bp):
GACCCTAAAACTATCCAAAAATGACATTTTTGCACCCAAACTTCCAAAAATTACATTTTTTAACC
TCGAACTTCCAAAAATTCCATTTTT
Found at i:35455053 original size:60 final size:59
Alignment explanation
Indices: 35454950--35455092 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 59
35454940 GAACTTCTTC
*
35454950 AAAATTACATTTTTAACCTTCGAACTTCCAAAAATTCCA-TTTTTGACCCTAAAACTTCCA
1 AAAATTACATTTTTAACC-TCAAACTTCCAAAAATTCCATTTTTTGA-CCTAAAACTTCCA
* * **
35455010 AAAATTACATTTTTGCACC-CAAACTTCCAAAAATTTCATTTTTTTGACCTCGAACTTCCA
1 AAAATTACATTTTT-AACCTCAAACTTCCAAAAATTCCA-TTTTTTGACCTAAAACTTCCA
* * *
35455070 AAACTTCCATTTTTAACCCCAAA
1 AAAATTACATTTTTAACCTCAAA
35455093 ACTCTTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
59 20 0.28
60 41 0.58
61 10 0.14
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTACATTTTTAACCTCAAACTTCCAAAAATTCCATTTTTTGACCTAAAACTTCCA
Found at i:35455245 original size:117 final size:117
Alignment explanation
Indices: 35455124--35455346 Score: 315
Period size: 117 Copynumber: 1.9 Consensus size: 117
35455114 CCCTTAGATG
* ** * ** *
35455124 TCCAAAAA-TCCCATTTTTGATCCCGATT-TTTCTAAAAATTATTGTTTTACCTTCGATTATCTA
1 TCCAAAAAGTCCC-GTTTTGATCCCGATTCTTTC-AAAAATTACCGTCTTACCCCCGATCATCTA
*
35455187 AAATGTCATTTTTAACCCCAAATTATCCCAAAATTACCATTTTTCCGTCGGGCA
64 AAATGTCATTTCTAACCCCAAATTATCCCAAAATTACCATTTTTCCGTCGGGCA
*
35455241 TCCAAAAAGTCCCGTTTTGATCCCGATTCTTTCGAAAATTACCGTCTTACCCCCGATCATCTAAA
1 TCCAAAAAGTCCCGTTTTGATCCCGATTCTTTCAAAAATTACCGTCTTACCCCCGATCATCTAAA
* *
35455306 ATGTCATTTCTAACCTCAAATTTTCCCAAAATTACCATTTT
66 ATGTCATTTCTAACCCCAAATTATCCCAAAATTACCATTTT
35455347 GCTCTTGAGA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
117 85 0.91
118 8 0.09
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.37
Consensus pattern (117 bp):
TCCAAAAAGTCCCGTTTTGATCCCGATTCTTTCAAAAATTACCGTCTTACCCCCGATCATCTAAA
ATGTCATTTCTAACCCCAAATTATCCCAAAATTACCATTTTTCCGTCGGGCA
Found at i:35457498 original size:161 final size:161
Alignment explanation
Indices: 35457196--35457674 Score: 699
Period size: 161 Copynumber: 3.0 Consensus size: 161
35457186 CAAAGAGATG
* *
35457196 AAATAGTGTGTTGTACTACTTGTGTTTCTTAATGATCACCTTTTTCAACAATCATTCATTCGCAA
1 AAATAGTGTGTTGTACTACTTGTGTTTCTTAATGA-CACCTTTTTCAGCAATCATTGATTCGCAA
* * * * * * * *
35457261 AAGTCTATTCTGATGGTAGGATGGTCTTCATTAGCTGTTACAATTGTTAAAATCATAAATTAATA
65 AGGTCTATCCTGGTGGTAGGATGGTCTTGATTGGCTGTTACAACTGTTAAAATCATAAATCAAGA
35457326 TATGATATAAAATTTAATAAATCATACACATA
130 TATGATATAAAATTTAATAAATCATACACATA
* * *
35457358 AAATAGTGTGTTGTACTATTTGTGTTTTTTAATGGACACCTTTTTCAGCAATTATTGATTCGCAA
1 AAATAGTGTGTTGTACTACTTGTGTTTCTTAAT-GACACCTTTTTCAGCAATCATTGATTCGCAA
* *
35457423 AGGTCTATCCTGGT-GTAAGATGGTCTTGATTGGATGTTACAACTGTTAAAATCATAAATCAAGA
65 AGGTCTATCCTGGTGGTAGGATGGTCTTGATTGGCTGTTACAACTGTTAAAATCATAAATCAAGA
* ** *
35457487 TATGATATAAAATTTAATAAACCATACAGGTG
130 TATGATATAAAATTTAATAAATCATACACATA
* *
35457519 AAATAGTGTGTTGTACTACTTGTGTTTCTTAATAGCCACCTTTTTCAGCAATCATTGATTCACAA
1 AAATAGTGTGTTGTACTACTTGTGTTTCTTAAT-GACACCTTTTTCAGCAATCATTGATTCGCAA
* * *
35457584 AGGTCTATCCTAGTGGTAGGATGGTCTGGATTGGCTGCTACAACTGTTAAAATCATAAATCAAGA
65 AGGTCTATCCTGGTGGTAGGATGGTCTTGATTGGCTGTTACAACTGTTAAAATCATAAATCAAGA
*
35457649 TATGATATAAATTTTAATAAATCATA
130 TATGATATAAAATTTAATAAATCATA
35457675 AACTAAGATC
Statistics
Matches: 283, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
161 143 0.51
162 138 0.49
163 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (161 bp):
AAATAGTGTGTTGTACTACTTGTGTTTCTTAATGACACCTTTTTCAGCAATCATTGATTCGCAAA
GGTCTATCCTGGTGGTAGGATGGTCTTGATTGGCTGTTACAACTGTTAAAATCATAAATCAAGAT
ATGATATAAAATTTAATAAATCATACACATA
Found at i:35459777 original size:29 final size:29
Alignment explanation
Indices: 35459745--35459801 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
35459735 TTCGAGGAAT
* *
35459745 TTGGGGTCAAAATTGAAATTTTGGAAAAC
1 TTGGGATCAAAATCGAAATTTTGGAAAAC
* * *
35459774 TTGGGATTAAGATCGAACTTTTGGAAAA
1 TTGGGATCAAAATCGAAATTTTGGAAAA
35459802 TTTGATGTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (29 bp):
TTGGGATCAAAATCGAAATTTTGGAAAAC
Found at i:35459887 original size:29 final size:28
Alignment explanation
Indices: 35459855--35459971 Score: 155
Period size: 28 Copynumber: 4.1 Consensus size: 28
35459845 GGTAATCTTA
35459855 GGATGTTCGAGGGTAAAATGATAATTTTT
1 GGATGTTCG-GGGTAAAATGATAATTTTT
* * *
35459884 GGATTTTTGGGGGTAAAATGGTAATTTTT
1 GGA-TGTTCGGGGTAAAATGATAATTTTT
* *
35459913 GGATGTTCGGGGAAAAAT-AGTAATATTT
1 GGATGTTCGGGGTAAAATGA-TAATTTTT
35459941 GGATGTTCGGGGTAAAATGATAATTTTT
1 GGATGTTCGGGGTAAAATGATAATTTTT
35459969 GGA
1 GGA
35459972 CATTCAAGGG
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
28 46 0.61
29 25 0.33
30 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.38
Consensus pattern (28 bp):
GGATGTTCGGGGTAAAATGATAATTTTT
Found at i:35459965 original size:56 final size:58
Alignment explanation
Indices: 35459855--35459993 Score: 167
Period size: 57 Copynumber: 2.4 Consensus size: 58
35459845 GGTAATCTTA
* * * * *
35459855 GGATGTTCGAGGGTAAAATGATAATTTTTGGATTTTTGGGGGTAAAATGGTAATTTTT
1 GGATGTTCGAGGGAAAAATGATAATATTTGGATTGTTCGGGGTAAAATGATAATTTTT
35459913 GGATGTTCG-GGGAAAAAT-AGTAATATTTGGA-TGTTCGGGGTAAAATGATAATTTTT
1 GGATGTTCGAGGGAAAAATGA-TAATATTTGGATTGTTCGGGGTAAAATGATAATTTTT
** * *
35459969 GGACATTCAAGGGAAAAATGGTAAT
1 GGATGTTCGAGGGAAAAATGATAAT
35459994 TTTTAGAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
56 29 0.42
57 31 0.45
58 9 0.13
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (58 bp):
GGATGTTCGAGGGAAAAATGATAATATTTGGATTGTTCGGGGTAAAATGATAATTTTT
Found at i:35459993 original size:29 final size:28
Alignment explanation
Indices: 35459811--35459997 Score: 160
Period size: 29 Copynumber: 6.6 Consensus size: 28
35459801 ATTTGATGTC
* * *
35459811 AAAAAT-GTGATTTTTGGAATTTTAGGGG
1 AAAAATGGTAATTTTTGG-ATGTTCGGGG
* * * *
35459839 CAAAAGGGTAATCTTAGGATGTTCGAGGG
1 AAAAATGGTAATTTTTGGATGTTCG-GGG
* * * *
35459868 TAAAATGATAATTTTTGGATTTTTGGGGG
1 AAAAATGGTAATTTTTGGA-TGTTCGGGG
*
35459897 TAAAATGGTAATTTTTGGATGTTCGGGG
1 AAAAATGGTAATTTTTGGATGTTCGGGG
* *
35459925 AAAAATAGTAATATTTGGATGTTCGGGG
1 AAAAATGGTAATTTTTGGATGTTCGGGG
* * ** *
35459953 TAAAATGATAATTTTTGGACATTCAAGGG
1 AAAAATGGTAATTTTTGGATGTTC-GGGG
35459982 AAAAATGGTAATTTTT
1 AAAAATGGTAATTTTT
35459998 AGAAATATTC
Statistics
Matches: 126, Mismatches: 29, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
28 59 0.47
29 63 0.50
30 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAAATGGTAATTTTTGGATGTTCGGGG
Found at i:35466870 original size:18 final size:18
Alignment explanation
Indices: 35466847--35466881 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35466837 CAGCCTATCA
35466847 TCAATTATGAA-TTAGTTT
1 TCAATTA-GAATTTAGTTT
35466865 TCAATTAGAATTTAGTT
1 TCAATTAGAATTTAGTT
35466882 ATTAGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (18 bp):
TCAATTAGAATTTAGTTT
Found at i:35467545 original size:16 final size:16
Alignment explanation
Indices: 35467524--35467555 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35467514 AGGCAGATTT
35467524 CCCACATGTCCCATGC
1 CCCACATGTCCCATGC
35467540 CCCACATGTCCCATGC
1 CCCACATGTCCCATGC
35467556 AAAATTCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.12, T:0.19
Consensus pattern (16 bp):
CCCACATGTCCCATGC
Found at i:35468553 original size:24 final size:24
Alignment explanation
Indices: 35468503--35468553 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35468493 TCGGACATAT
** **
35468503 ATTTGTATTTATCTTATACTTGTA
1 ATTTGTACGTATCTTATACTTACA
35468527 ATTTGTACGTATCTTATACTTACA
1 ATTTGTACGTATCTTATACTTACA
35468551 ATT
1 ATT
35468554 ATATTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (24 bp):
ATTTGTACGTATCTTATACTTACA
Found at i:35483594 original size:21 final size:21
Alignment explanation
Indices: 35483570--35483636 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
35483560 AAGCACAATT
35483570 GTATAAACTAGAGAACAAAAA
1 GTATAAACTAGAGAACAAAAA
* **
35483591 GTATAGA--AG-GAAGCACAATT
1 GTATAAACTAGAGAA-CA-AAAA
35483611 GTATAAACTAGAGAACAAAAA
1 GTATAAACTAGAGAACAAAAA
35483632 GTATA
1 GTATA
35483637 CACACAGACA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 3 0.09
19 4 0.11
20 8 0.23
21 13 0.37
22 4 0.11
23 3 0.09
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (21 bp):
GTATAAACTAGAGAACAAAAA
Found at i:35483600 original size:41 final size:41
Alignment explanation
Indices: 35483552--35483636 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
35483542 AAAAGCAATA
35483552 ATAGAAGGAAGCACAATTGTATAAACTAGAGAACAAAAAGT
1 ATAGAAGGAAGCACAATTGTATAAACTAGAGAACAAAAAGT
35483593 ATAGAAGGAAGCACAATTGTATAAACTAGAGAACAAAAAGT
1 ATAGAAGGAAGCACAATTGTATAAACTAGAGAACAAAAAGT
35483634 ATA
1 ATA
35483637 CACACAGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.18
Consensus pattern (41 bp):
ATAGAAGGAAGCACAATTGTATAAACTAGAGAACAAAAAGT
Found at i:35483628 original size:20 final size:20
Alignment explanation
Indices: 35483564--35483628 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
35483554 AGAAGGAAGC
35483564 ACAATTGTATAAACTAGAGA
1 ACAATTGTATAAACTAGAGA
** ** *
35483584 ACAAAAAGTATAGAAGGA-AGC
1 AC-AATTGTATA-AACTAGAGA
35483605 ACAATTGTATAAACTAGAGA
1 ACAATTGTATAAACTAGAGA
35483625 ACAA
1 ACAA
35483629 AAAGTATACA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 11 0.34
22 3 0.09
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.18
Consensus pattern (20 bp):
ACAATTGTATAAACTAGAGA
Found at i:35484236 original size:6 final size:6
Alignment explanation
Indices: 35484227--35484251 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35484217 TGGGATTGGC
35484227 ATGAAG ATGAAG ATGAAG ATGAAG A
1 ATGAAG ATGAAG ATGAAG ATGAAG A
35484252 AGTAACAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
ATGAAG
Found at i:35485835 original size:21 final size:21
Alignment explanation
Indices: 35485811--35485854 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
35485801 AAAATTGTTG
*
35485811 TTTTGTTGTTTTCTTGATATT
1 TTTTATTGTTTTCTTGATATT
* *
35485832 TTTTATTGTTTTGTTGTTATT
1 TTTTATTGTTTTCTTGATATT
35485853 TT
1 TT
35485855 CTGACTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.02, G:0.14, T:0.75
Consensus pattern (21 bp):
TTTTATTGTTTTCTTGATATT
Found at i:35485849 original size:32 final size:32
Alignment explanation
Indices: 35485804--35485865 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
35485794 TGAAAAAAAA
*
35485804 ATTGTTGTTTTGTTGTTTTCTTGA-TATTTTTT
1 ATTGTTGTTTTGTTATTTTC-TGACTATTTTTT
35485836 ATTGTT-TTGTTGTTATTTTCTGACTATTTT
1 ATTGTTGTT-TTGTTATTTTCTGACTATTTT
35485866 GCTACGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.11, C:0.05, G:0.15, T:0.69
Consensus pattern (32 bp):
ATTGTTGTTTTGTTATTTTCTGACTATTTTTT
Found at i:35495129 original size:7 final size:7
Alignment explanation
Indices: 35495117--35495143 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
35495107 TGCACGGCAA
35495117 CAGCGTG
1 CAGCGTG
35495124 CAGCGTG
1 CAGCGTG
35495131 CAGCGTG
1 CAGCGTG
35495138 CAGCGT
1 CAGCGT
35495144 ACTTGGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.41, T:0.15
Consensus pattern (7 bp):
CAGCGTG
Found at i:35496826 original size:6 final size:6
Alignment explanation
Indices: 35496815--35496900 Score: 74
Period size: 6 Copynumber: 15.0 Consensus size: 6
35496805 TTGGATTTAT
* * *
35496815 TTTAAA TTTAAA TTTTAAA -GTAAA TTTAAA TTT--G TTAAAA TTTAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
35496861 TTTAAA --CAAA TTTAAA TTTAAA TTTATG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35496901 ATTATTCTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
4 5 0.08
5 4 0.06
6 47 0.76
7 6 0.10
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:35496871 original size:16 final size:15
Alignment explanation
Indices: 35496818--35496882 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 15
35496808 GATTTATTTT
35496818 AAATTTAAATTTTAAA
1 AAATTTAAA-TTTAAA
**
35496834 GTAAATTTAAATTTGTTA
1 --AAATTTAAATTT-AAA
35496852 AAATTTAAATTTAAA
1 AAATTTAAATTTAAA
35496867 CAAATTTAAATTTAAA
1 -AAATTTAAATTTAAA
35496883 TTTATGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.02
16 27 0.66
17 3 0.07
18 10 0.24
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTAAA
Found at i:35496905 original size:18 final size:18
Alignment explanation
Indices: 35496871--35496905 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35496861 TTTAAACAAA
*
35496871 TTTAAATTTAAATTTATG
1 TTTAAATTTAAAATTATG
35496889 TTTAAATTTAAAATTAT
1 TTTAAATTTAAAATTAT
35496906 TCTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAATTTAAAATTATG
Found at i:35497098 original size:13 final size:13
Alignment explanation
Indices: 35497080--35497104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35497070 AGCCGTCAGC
35497080 GCCACGTCAGCAT
1 GCCACGTCAGCAT
35497093 GCCACGTCAGCA
1 GCCACGTCAGCA
35497105 CTATCTGCTA
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:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (13 bp):
GCCACGTCAGCAT
Found at i:35515700 original size:9 final size:9
Alignment explanation
Indices: 35515672--35515701 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
35515662 CTTAAATAGC
35515672 ATTAATAAT
1 ATTAATAAT
*
35515681 AATAATAAT
1 ATTAATAAT
35515690 ATTAATAAT
1 ATTAATAAT
35515699 ATT
1 ATT
35515702 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTAATAAT
Found at i:35516848 original size:30 final size:30
Alignment explanation
Indices: 35516812--35516949 Score: 126
Period size: 30 Copynumber: 4.7 Consensus size: 30
35516802 TTTGCCCCTT
35516812 CAAAAATTCTATTTTTGACCTCGAAACTTC
1 CAAAAATTCTATTTTTGACCTCGAAACTTC
* * *
35516842 CAAAAATTATATTTTTGACCCTC-AAATTTT
1 CAAAAATTCTATTTTTGA-CCTCGAAACTTC
* * *
35516872 CAAAAATTCCA-TTTTAACC-CTAAAACTTC
1 CAAAAATTCTATTTTTGACCTC-GAAACTTC
* *
35516901 CAAAAAGTAC-ATTTTTGCCCTCG-AACTTC
1 CAAAAA-TTCTATTTTTGACCTCGAAACTTC
35516930 CAAAAATT-TGATTTTTGACC
1 CAAAAATTCT-ATTTTTGACC
35516950 CCAAAATTTC
Statistics
Matches: 86, Mismatches: 14, Indels: 17
0.74 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 3 0.03
29 38 0.44
30 39 0.45
31 5 0.06
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (30 bp):
CAAAAATTCTATTTTTGACCTCGAAACTTC
Found at i:35516856 original size:29 final size:29
Alignment explanation
Indices: 35516782--35516996 Score: 153
Period size: 29 Copynumber: 7.5 Consensus size: 29
35516772 TGACCCCTAA
*
35516782 AAACTTCCAAAAATTACATTTTTG--CCC
1 AAACTTCCAAAAATTATATTTTTGACCCC
* *
35516809 ---CTT-CAAAAATTCTATTTTTGACCTCG
1 AAACTTCCAAAAATTATATTTTTGACC-CC
35516835 AAACTTCCAAAAATTATATTTTTGACCCTC
1 AAACTTCCAAAAATTATATTTTTGACCC-C
* * ** * *
35516865 AAATTTTCAAAAATTCCA-TTTTAACCCTA
1 AAACTTCCAAAAATTATATTTTTGACCC-C
* *
35516894 AAACTTCCAAAAAGTACATTTTTG-CCCTC
1 AAACTTCCAAAAATTATATTTTTGACCC-C
*
35516923 GAACTTCCAAAAATT-TGATTTTTGACCCC
1 AAACTTCCAAAAATTAT-ATTTTTGACCCC
* * *
35516952 AAAATTTCACAAAATTAT-TTTTTTACCCC
1 AAACTTCCA-AAAATTATATTTTTGACCCC
*
35516981 CAACATTCCAAAAATT
1 AAAC-TTCCAAAAATT
35516997 CCATTTTGAC
Statistics
Matches: 147, Mismatches: 27, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
23 15 0.10
24 3 0.02
25 1 0.01
26 1 0.01
29 76 0.52
30 50 0.34
31 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAAATTATATTTTTGACCCC
Found at i:35517003 original size:59 final size:58
Alignment explanation
Indices: 35516768--35517008 Score: 176
Period size: 59 Copynumber: 4.2 Consensus size: 58
35516758 CAGGAATTGT
** * *
35516768 ATTTTGACCCCTAAAAACTTCCAAAAATTACATTTTT--GCCC--C-TT-CAAAAATTCT
1 ATTTTGACCCC--AAAACTTCCAAAAATTATTTTTTTACCCCCAACATTCCAAAAATTCC
* * * * *
35516822 ATTTTTGACCTCGAAACTTCCAAAAATTATATTTTTGACCCTCAA-ATTTTCAAAAATTCC
1 A-TTTTGACCCCAAAACTTCCAAAAATTAT-TTTTTTACCCCCAACA-TTCCAAAAATTCC
* * * ** * * **
35516882 ATTTTAACCCTAAAACTTCCAAAAAGTACATTTTTGCCCTCGAAC-TTCCAAAAATTTG
1 ATTTTGACCCCAAAACTTCCAAAAATTATTTTTTTACCC-CCAACATTCCAAAAATTCC
*
35516940 ATTTTTGACCCCAAAA-TTTCACAAAATTATTTTTTTACCCCCAACATTCCAAAAATTCC
1 A-TTTTGACCCCAAAACTTCCA-AAAATTATTTTTTTACCCCCAACATTCCAAAAATTCC
35516999 ATTTTGACCC
1 ATTTTGACCC
35517009 TGATGCCTCC
Statistics
Matches: 141, Mismatches: 32, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
53 16 0.11
54 5 0.04
55 9 0.06
56 2 0.01
58 35 0.25
59 64 0.45
60 10 0.07
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (58 bp):
ATTTTGACCCCAAAACTTCCAAAAATTATTTTTTTACCCCCAACATTCCAAAAATTCC
Found at i:35517023 original size:28 final size:27
Alignment explanation
Indices: 35516991--35517070 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 27
35516981 CAACATTCCA
35516991 AAAATTCCATTTTGACCCTGATGCCTCC
1 AAAATTCCATTTTGACCCTGATG-CTCC
* *
35517019 AAAATTACCATTTT-ACCCTTGGATGTTTC
1 AAAATT-CCATTTTGACCC-T-GATGCTCC
*
35517048 AAAATTCCATTTTTGATCCTGAT
1 AAAATTCCA-TTTTGACCCTGAT
35517071 TTTTTCAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
28 16 0.36
29 21 0.48
30 7 0.16
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (27 bp):
AAAATTCCATTTTGACCCTGATGCTCC
Found at i:35517050 original size:29 final size:29
Alignment explanation
Indices: 35517018--35517100 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
35517008 CTGATGCCTC
35517018 CAAAATTACCATTTTACCCTTGGATGTTT
1 CAAAATTACCATTTTACCCTTGGATGTTT
* *
35517047 CAAAATT-CCATTTTTGATCC-T-GATTTTTT
1 CAAAATTACCA-TTTT-ACCCTTGGA-TGTTT
* *
35517076 CAAAATTACCGTTTTACCCTCGGAT
1 CAAAATTACCATTTTACCCTTGGAT
35517101 ATCTAAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
28 8 0.19
29 28 0.65
30 7 0.16
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (29 bp):
CAAAATTACCATTTTACCCTTGGATGTTT
Found at i:35517062 original size:58 final size:57
Alignment explanation
Indices: 35516991--35517100 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 57
35516981 CAACATTCCA
*
35516991 AAAATTCCATTTTGACCCTGATGCCTCCAAAATTACCATTTTACCCTTGGATGTTTC
1 AAAATTCCATTTTGACCCTGATGCCTCCAAAATTACCATTTTACCCTCGGATGTTTC
* *** * *
35517048 AAAATTCCATTTTTGATCCTGATTTTTTCAAAATTACCGTTTTACCCTCGGAT
1 AAAATTCCA-TTTTGACCCTGATGCCTCCAAAATTACCATTTTACCCTCGGAT
35517101 ATCTAAAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 9 0.20
58 36 0.80
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (57 bp):
AAAATTCCATTTTGACCCTGATGCCTCCAAAATTACCATTTTACCCTCGGATGTTTC
Found at i:35524120 original size:50 final size:49
Alignment explanation
Indices: 35524042--35524337 Score: 183
Period size: 50 Copynumber: 5.9 Consensus size: 49
35524032 GAAAGATATG
* *
35524042 AAGGGAAAGATCTAAGATCGCAATGGCGGATCCAGTACCACGAAGATGCAA
1 AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGA--CAA
* * * * * *
35524093 AAGGGAAAGGTCCAAG-TCACAACGGCGGA-CCGTGTACCTCAGAAGACAA
1 AAGGGAAAGATCTAAGACCGCAACGGCGGATCC-AGTACCAC-GAAGACAA
** * * * * *
35524142 GAAAAGAAAGATTTAAG-CCGCAACGACGAATCCAGTACCATGAAGACATG
1 -AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGACA-A
**
35524192 AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCATAAAGATACAA
1 AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAG--ACAA
* * * * * *
35524243 AAGGGAAAGGTTTAAG-TCGCAATGGCAGA-CCATGTACCTCAGAAGACAGGA
1 AAGGGAAAGATCTAAGACCGCAACGGCGGATCCA-GTACCAC-GAAGACA--A
* * * * *
35524294 AA-GGAAAGATTTAAG-CCGCAACGACGAATCTAGTATCACGAAGA
1 AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGA
35524338 TTTGAAAGGG
Statistics
Matches: 189, Mismatches: 43, Indels: 28
0.73 0.17 0.11
Matches are distributed among these distances:
49 36 0.19
50 107 0.57
51 43 0.23
52 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.14
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGACAA
Found at i:35524310 original size:150 final size:150
Alignment explanation
Indices: 35524034--35524351 Score: 465
Period size: 150 Copynumber: 2.1 Consensus size: 150
35524024 CGGTACTAGA
* * * *
35524034 AAGATATGAAGGGAAAGATCTAAGATCGCAATGGCGGATCCAGTACCACGAAGATGCAAAAGGGA
1 AAGATATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
* *
35524099 AAGGTCCAAGTCACAACGGCGGACCGTGTACCTCAGAAGACAAGAAAAGAAAGATTTAAGCCGCA
66 AAGGTCCAAGTCACAACGGCAGACCATGTACCTCAGAAGACAAGAAAAGAAAGATTTAAGCCGCA
*
35524164 ACGACGAATCCAGTACCATG
131 ACGACGAATCCAGTACCACG
* *
35524184 AAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGGA
1 AAGATATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
** * * * *
35524249 AAGGTTTAAGTCGCAATGGCAGACCATGTACCTCAGAAGACAGGAAAGGAAAGATTTAAGCCGCA
66 AAGGTCCAAGTCACAACGGCAGACCATGTACCTCAGAAGACAAGAAAAGAAAGATTTAAGCCGCA
* *
35524314 ACGACGAATCTAGTATCACG
131 ACGACGAATCCAGTACCACG
*
35524334 AAGATTTGAAAGGGAAAG
1 AAGATATG-AAGGGAAAG
35524352 TTTTAAGTCG
Statistics
Matches: 148, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
150 139 0.94
151 9 0.06
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (150 bp):
AAGATATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
AAGGTCCAAGTCACAACGGCAGACCATGTACCTCAGAAGACAAGAAAAGAAAGATTTAAGCCGCA
ACGACGAATCCAGTACCACG
Found at i:35524380 original size:100 final size:101
Alignment explanation
Indices: 35524183--35524386 Score: 232
Period size: 100 Copynumber: 2.0 Consensus size: 101
35524173 CCAGTACCAT
* * * * *
35524183 GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGG
1 GAAGACAGGAAAGGAAAGATCTAAGACCGCAACGACGAATCCAGTACCACAAAGATACAAAAGGG
*
35524248 AAAGGTTTAAGTCGCAATGGCAGACCATGTACCTCA
66 AAAGGTTTAAGTCGCAATGGCAGACCAGGTACCTCA
* * * * ***
35524284 GAAGACAGGAAAGGAAAGATTTAAG-CCGCAACGACGAATCTAGTATCACGAAGATTTGAAAGGG
1 GAAGACAGGAAAGGAAAGATCTAAGACCGCAACGACGAATCCAGTACCACAAAGATACAAAAGGG
* * * *
35524348 AAAGTTTTAAGTCGCGATGGC-GAGCCCGGTACCTTA
66 AAAGGTTTAAGTCGCAATGGCAGA-CCAGGTACCTCA
35524384 GAA
1 GAA
35524387 ACATGACGAG
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
99 2 0.02
100 61 0.72
101 22 0.26
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (101 bp):
GAAGACAGGAAAGGAAAGATCTAAGACCGCAACGACGAATCCAGTACCACAAAGATACAAAAGGG
AAAGGTTTAAGTCGCAATGGCAGACCAGGTACCTCA
Done.